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[Gsrc-commit] trunk r3732: big change, add all bioinfomatics progs
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From: |
Carl Hansen |
|
Subject: |
[Gsrc-commit] trunk r3732: big change, add all bioinfomatics progs |
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Date: |
Fri, 17 Jun 2016 19:57:47 +0000 (UTC) |
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User-agent: |
Bazaar (2.6b2) |
------------------------------------------------------------
revno: 3732
revision-id: address@hidden
parent: address@hidden
committer: address@hidden
branch nick: trunk
timestamp: Fri 2016-06-17 12:57:40 -0700
message:
big change, add all bioinfomatics progs
removed:
pkg/external/python2/ python2-20160617013639-z5fu1hm2di316w5v-47
pkg/external/python2/Makefile makefile-20160617013639-z5fu1hm2di316w5v-112
added:
pkg/bio/ bio-20160617195624-kwz1a09vkg4le6fu-1
pkg/bio/aragorn/ aragorn-20160617195624-kwz1a09vkg4le6fu-2
pkg/bio/aragorn/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-67
pkg/bio/aragorn/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-68
pkg/bio/bamtools/ bamtools-20160617195624-kwz1a09vkg4le6fu-3
pkg/bio/bamtools/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-69
pkg/bio/bamtools/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-70
pkg/bio/barrnap/ barrnap-20160617195624-kwz1a09vkg4le6fu-4
pkg/bio/barrnap/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-71
pkg/bio/barrnap/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-72
pkg/bio/bedtools/ bedtools-20160617195624-kwz1a09vkg4le6fu-5
pkg/bio/bedtools/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-73
pkg/bio/bedtools/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-74
pkg/bio/bfast/ bfast-20160617195624-kwz1a09vkg4le6fu-6
pkg/bio/bfast/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-75
pkg/bio/bfast/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-76
pkg/bio/bismark/ bismark-20160617195624-kwz1a09vkg4le6fu-7
pkg/bio/bismark/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-77
pkg/bio/bismark/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-78
pkg/bio/bowtie/ bowtie-20160617195624-kwz1a09vkg4le6fu-8
pkg/bio/bowtie/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-79
pkg/bio/bowtie/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-80
pkg/bio/breakway/ breakway-20160617195624-kwz1a09vkg4le6fu-9
pkg/bio/breakway/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-81
pkg/bio/breakway/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-82
pkg/bio/bwa/ bwa-20160617195624-kwz1a09vkg4le6fu-10
pkg/bio/bwa/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-83
pkg/bio/bwa/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-84
pkg/bio/cd-hit/ cdhit-20160617195624-kwz1a09vkg4le6fu-11
pkg/bio/cd-hit/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-85
pkg/bio/cd-hit/files/ files-20160617195624-kwz1a09vkg4le6fu-86
pkg/bio/cd-hit/files/cd-hit-v4.6.1-2012-08-27-fix-max-sequences.diff
cdhitv4.6.120120827f-20160617195624-kwz1a09vkg4le6fu-203
pkg/bio/cd-hit/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-87
pkg/bio/clustal-omega/ clustalomega-20160617195624-kwz1a09vkg4le6fu-12
pkg/bio/clustal-omega/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-88
pkg/bio/clustal-omega/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-89
pkg/bio/clustalw/ clustalw-20160617195624-kwz1a09vkg4le6fu-13
pkg/bio/clustalw/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-90
pkg/bio/clustalw/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-91
pkg/bio/csblast/ csblast-20160617195624-kwz1a09vkg4le6fu-14
pkg/bio/csblast/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-92
pkg/bio/csblast/files/ files-20160617195624-kwz1a09vkg4le6fu-93
pkg/bio/csblast/files/csblast-2.2.3-add-missing-targets.diff
csblast2.2.3addmissi-20160617195624-kwz1a09vkg4le6fu-204
pkg/bio/csblast/files/csblast-2.2.3-fix-redeclaration.diff
csblast2.2.3fixredec-20160617195624-kwz1a09vkg4le6fu-205
pkg/bio/csblast/files/csblast-2.2.3-makefile-modes.diff
csblast2.2.3makefile-20160617195624-kwz1a09vkg4le6fu-206
pkg/bio/csblast/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-94
pkg/bio/cufflinks/ cufflinks-20160617195624-kwz1a09vkg4le6fu-15
pkg/bio/cufflinks/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-95
pkg/bio/cufflinks/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-96
pkg/bio/dnaa/ dnaa-20160617195624-kwz1a09vkg4le6fu-16
pkg/bio/dnaa/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-97
pkg/bio/dnaa/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-98
pkg/bio/e-pcr/ epcr-20160617195624-kwz1a09vkg4le6fu-17
pkg/bio/e-pcr/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-99
pkg/bio/e-pcr/files/ files-20160617195624-kwz1a09vkg4le6fu-100
pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff
epcr2.3.12includestr-20160617195624-kwz1a09vkg4le6fu-207
pkg/bio/e-pcr/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-101
pkg/bio/emboss/ emboss-20160617195624-kwz1a09vkg4le6fu-18
pkg/bio/emboss/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-102
pkg/bio/emboss/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-103
pkg/bio/fasttree/ fasttree-20160617195624-kwz1a09vkg4le6fu-19
pkg/bio/fasttree/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-104
pkg/bio/fasttree/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-105
pkg/bio/fastx-toolkit/ fastxtoolkit-20160617195624-kwz1a09vkg4le6fu-20
pkg/bio/fastx-toolkit/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-106
pkg/bio/fastx-toolkit/sha256sums
sha256sums-20160617195624-kwz1a09vkg4le6fu-107
pkg/bio/fsa/ fsa-20160617195624-kwz1a09vkg4le6fu-21
pkg/bio/fsa/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-108
pkg/bio/fsa/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-109
pkg/bio/hmmer/ hmmer-20160617195624-kwz1a09vkg4le6fu-22
pkg/bio/hmmer/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-110
pkg/bio/hmmer/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-111
pkg/bio/hyphy/ hyphy-20160617195624-kwz1a09vkg4le6fu-23
pkg/bio/hyphy/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-112
pkg/bio/hyphy/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-113
pkg/bio/infernal/ infernal-20160617195624-kwz1a09vkg4le6fu-24
pkg/bio/infernal/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-114
pkg/bio/infernal/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-115
pkg/bio/jellyfish/ jellyfish-20160617195624-kwz1a09vkg4le6fu-25
pkg/bio/jellyfish/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-116
pkg/bio/jellyfish/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-117
pkg/bio/kraken/ kraken-20160617195624-kwz1a09vkg4le6fu-26
pkg/bio/kraken/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-118
pkg/bio/kraken/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-119
pkg/bio/macs/ macs-20160617195624-kwz1a09vkg4le6fu-27
pkg/bio/macs/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-120
pkg/bio/macs/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-121
pkg/bio/mafft/ mafft-20160617195624-kwz1a09vkg4le6fu-28
pkg/bio/mafft/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-122
pkg/bio/mafft/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-123
pkg/bio/melting/ melting-20160617195624-kwz1a09vkg4le6fu-29
pkg/bio/melting/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-124
pkg/bio/melting/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-125
pkg/bio/minced/ minced-20160617195624-kwz1a09vkg4le6fu-30
pkg/bio/minced/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-126
pkg/bio/minced/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-127
pkg/bio/moods/ moods-20160617195624-kwz1a09vkg4le6fu-31
pkg/bio/moods/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-128
pkg/bio/moods/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-129
pkg/bio/mrbayes/ mrbayes-20160617195624-kwz1a09vkg4le6fu-32
pkg/bio/mrbayes/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-130
pkg/bio/mrbayes/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-131
pkg/bio/mummer/ mummer-20160617195624-kwz1a09vkg4le6fu-33
pkg/bio/mummer/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-132
pkg/bio/mummer/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-133
pkg/bio/ncbi-blast/ ncbiblast-20160617195624-kwz1a09vkg4le6fu-34
pkg/bio/ncbi-blast/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-134
pkg/bio/ncbi-blast/files/ files-20160617195624-kwz1a09vkg4le6fu-135
pkg/bio/ncbi-blast/files/ncbi-blast-2.2.29+-src-include-typeinfo.diff
ncbiblast2.2.29srcin-20160617195624-kwz1a09vkg4le6fu-208
pkg/bio/ncbi-blast/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-136
pkg/bio/ncbi-tools/ ncbitools-20160617195624-kwz1a09vkg4le6fu-35
pkg/bio/ncbi-tools/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-137
pkg/bio/ncbi-tools/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-138
pkg/bio/newick-utils/ newickutils-20160617195624-kwz1a09vkg4le6fu-36
pkg/bio/newick-utils/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-139
pkg/bio/newick-utils/files/ files-20160617195624-kwz1a09vkg4le6fu-140
pkg/bio/newick-utils/files/newick-utils-1.6-compile-w-lua-5.2.patch
newickutils1.6compil-20160617195624-kwz1a09vkg4le6fu-209
pkg/bio/newick-utils/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-141
pkg/bio/oma/ oma-20160617195624-kwz1a09vkg4le6fu-37
pkg/bio/oma/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-142
pkg/bio/oma/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-143
pkg/bio/openms/ openms-20160617195624-kwz1a09vkg4le6fu-38
pkg/bio/openms/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-144
pkg/bio/openms/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-145
pkg/bio/pagan-msa/ paganmsa-20160617195624-kwz1a09vkg4le6fu-39
pkg/bio/pagan-msa/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-146
pkg/bio/pagan-msa/files/ files-20160617195624-kwz1a09vkg4le6fu-147
pkg/bio/pagan-msa/files/pagan-msa-20121025-include-unistd_h.patch
paganmsa20121025incl-20160617195624-kwz1a09vkg4le6fu-210
pkg/bio/pagan-msa/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-148
pkg/bio/pfamscan/ pfamscan-20160617195624-kwz1a09vkg4le6fu-40
pkg/bio/pfamscan/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-149
pkg/bio/pfamscan/PfamScan.tar.gz
pfamscan.tar.gz-20160617195624-kwz1a09vkg4le6fu-150
pkg/bio/pfamscan/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-151
pkg/bio/phyml/ phyml-20160617195624-kwz1a09vkg4le6fu-41
pkg/bio/phyml/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-152
pkg/bio/phyml/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-153
pkg/bio/prank-msa/ prankmsa-20160617195624-kwz1a09vkg4le6fu-42
pkg/bio/prank-msa/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-154
pkg/bio/prank-msa/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-155
pkg/bio/primer3/ primer3-20160617195624-kwz1a09vkg4le6fu-43
pkg/bio/primer3/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-156
pkg/bio/primer3/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-157
pkg/bio/prodigal/ prodigal-20160617195624-kwz1a09vkg4le6fu-44
pkg/bio/prodigal/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-158
pkg/bio/prodigal/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-159
pkg/bio/prokka/ prokka-20160617195624-kwz1a09vkg4le6fu-45
pkg/bio/prokka/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-160
pkg/bio/prokka/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-161
pkg/bio/provean/ provean-20160617195624-kwz1a09vkg4le6fu-46
pkg/bio/provean/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-162
pkg/bio/provean/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-163
pkg/bio/pscan/ pscan-20160617195624-kwz1a09vkg4le6fu-47
pkg/bio/pscan/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-164
pkg/bio/pscan/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-165
pkg/bio/qmmraxml/ qmmraxml-20160617195624-kwz1a09vkg4le6fu-48
pkg/bio/qmmraxml/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-166
pkg/bio/qmmraxml/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-167
pkg/bio/quake/ quake-20160617195624-kwz1a09vkg4le6fu-49
pkg/bio/quake/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-168
pkg/bio/quake/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-169
pkg/bio/raxml/ raxml-20160617195624-kwz1a09vkg4le6fu-50
pkg/bio/raxml/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-170
pkg/bio/raxml/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-171
pkg/bio/reapr/ reapr-20160617195624-kwz1a09vkg4le6fu-51
pkg/bio/reapr/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-172
pkg/bio/reapr/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-173
pkg/bio/rnaz/ rnaz-20160617195624-kwz1a09vkg4le6fu-52
pkg/bio/rnaz/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-174
pkg/bio/rnaz/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-175
pkg/bio/samtools/ samtools-20160617195624-kwz1a09vkg4le6fu-53
pkg/bio/samtools/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-176
pkg/bio/samtools/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-177
pkg/bio/seq_crumbs/ seq_crumbs-20160617195624-kwz1a09vkg4le6fu-54
pkg/bio/seq_crumbs/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-178
pkg/bio/seq_crumbs/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-179
pkg/bio/seqsuite/ seqsuite-20160617195624-kwz1a09vkg4le6fu-55
pkg/bio/seqsuite/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-180
pkg/bio/seqsuite/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-181
pkg/bio/seqtk/ seqtk-20160617195624-kwz1a09vkg4le6fu-56
pkg/bio/seqtk/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-182
pkg/bio/seqtk/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-183
pkg/bio/slimsuite/ slimsuite-20160617195624-kwz1a09vkg4le6fu-57
pkg/bio/slimsuite/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-184
pkg/bio/slimsuite/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-185
pkg/bio/smalt/ smalt-20160617195624-kwz1a09vkg4le6fu-58
pkg/bio/smalt/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-186
pkg/bio/smalt/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-187
pkg/bio/snpomatic/ snpomatic-20160617195624-kwz1a09vkg4le6fu-59
pkg/bio/snpomatic/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-188
pkg/bio/t-coffee/ tcoffee-20160617195624-kwz1a09vkg4le6fu-60
pkg/bio/t-coffee/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-189
pkg/bio/t-coffee/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-190
pkg/bio/tabix/ tabix-20160617195624-kwz1a09vkg4le6fu-61
pkg/bio/tabix/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-191
pkg/bio/tabix/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-192
pkg/bio/tophat/ tophat-20160617195624-kwz1a09vkg4le6fu-62
pkg/bio/tophat/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-193
pkg/bio/tophat/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-194
pkg/bio/treebest/ treebest-20160617195624-kwz1a09vkg4le6fu-63
pkg/bio/treebest/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-195
pkg/bio/treebest/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-196
pkg/bio/trimal/ trimal-20160617195624-kwz1a09vkg4le6fu-64
pkg/bio/trimal/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-197
pkg/bio/trimal/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-198
pkg/bio/weeder/ weeder-20160617195624-kwz1a09vkg4le6fu-65
pkg/bio/weeder/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-199
pkg/bio/weeder/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-200
pkg/bio/weederh/ weederh-20160617195624-kwz1a09vkg4le6fu-66
pkg/bio/weederh/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-201
pkg/bio/weederh/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-202
modified:
pkg/other/libffi/Makefile makefile-20160617021831-zlvtnp07nqas2p6o-3
pkg/other/libffi/config.mk config.mk-20160617021834-1gawmrqbecrjehnr-1
=== added directory 'pkg/bio'
=== added directory 'pkg/bio/aragorn'
=== added file 'pkg/bio/aragorn/Makefile'
--- a/pkg/bio/aragorn/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/aragorn/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,60 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = ARAGORN
+GARNAME = aragorn
+GARVERSION = 1.2.36
+HOME_URL = http://mbio-serv2.mbioekol.lu.se/ARAGORN/
+DESCRIPTION = tRNA (and tmRNA) detection
+define BLURB
+ARAGORN identifies tRNA and tmRNA genes by predicting their secondary
+structure and performing homology comparisons with consensus
+sequences.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1093/nar/gkh152
+
+######################################################################
+
+MASTER_SITES = http://mbio-serv2.mbioekol.lu.se/
+MASTER_SUBDIR = $(NAME)/Downloads/
+DISTNAME = $(GARNAME)$(GARVERSION)
+DISTFILES = $(DISTNAME).tgz
+BUILD_SCRIPTS = bin
+INSTALL_SCRIPTS = bin man
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+CFLAGS = -O3 -ffast-math -finline-functions
+
+build-bin:
+ $(CC) $(CFLAGS) -o $(WORKSRC)/$(GARNAME) $(WORKSRC)/$(DISTNAME).c
+ $(MAKECOOKIE)
+
+install-bin:
+ $(INSTALL_BIN) $(WORKSRC)/$(GARNAME)
+ $(MAKECOOKIE)
+
+install-man:
+ $(INSTALL_MAN) $(WORKSRC)/$(GARNAME).1
+ $(MAKECOOKIE)
=== added file 'pkg/bio/aragorn/sha256sums'
--- a/pkg/bio/aragorn/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/aragorn/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+ab06032589e45aa002f8616333568e9ab11034b3a675f922421e5f1c3e95e7b5
download/aragorn1.2.36.tgz
=== added directory 'pkg/bio/bamtools'
=== added file 'pkg/bio/bamtools/Makefile'
--- a/pkg/bio/bamtools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bamtools/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = BamTools
+GARNAME = bamtools
+GARVERSION = 2.3.0
+HOME_URL = https://github.com/pezmaster31/bamtools
+DESCRIPTION = A library and toolkit for handling BAM files
+define BLURB
+BamTools provides both an API and a user-level toolkit for handling and
+processing BAM files.
+endef
+LICENSE = Expat License
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = pezmaster31/$(GARNAME)/archive/
+DISTFILES = v$(GARVERSION).tar.gz
+SIGFILES =
+WORKOBJ = $(WORKDIR)/$(DISTNAME)-build
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
=== added file 'pkg/bio/bamtools/sha256sums'
--- a/pkg/bio/bamtools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bamtools/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af
download/v2.3.0.tar.gz
=== added directory 'pkg/bio/barrnap'
=== added file 'pkg/bio/barrnap/Makefile'
--- a/pkg/bio/barrnap/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/barrnap/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,58 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Barrnap
+GARNAME = barrnap
+GARVERSION = 0.5
+HOME_URL = http://www.vicbioinformatics.com/software.barrnap.shtml
+DESCRIPTION = Basic rapid ribosomal RNA predictor
+define BLURB
+Barrnap predicts the location of ribosomal RNA genes.
+endef
+LICENSE = GPLv3
+CITE =
+
+######################################################################
+
+MASTER_SITES = http://www.vicbioinformatics.com/
+MASTER_SUBDIR =
+DISTFILES = $(DISTNAME).tar.gz
+INSTALL_SCRIPTS = db script
+
+BUILDDEPS =
+LIBDEPS = hmmer
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+pre-install:
+ sed -i '16s|.*|my \$$DBDIR = "$(packageprefix)/share/$(GARNAME)/db";|'
$(WORKSRC)/bin/$(GARNAME)
+ sed -i '18s|.*|my \$$NHMMER = "$(prefix)/bin/nhmmer";|'
$(WORKSRC)/bin/$(GARNAME)
+ $(MAKECOOKIE)
+
+install-db:
+ install -d $(packageprefix)/share/$(GARNAME)/db
+ for f in $(WORKSRC)/db/*.hmm; do \
+ install -m644 $$f
$(packageprefix)/share/$(GARNAME)/db/`basename $$f`; \
+ done
+ $(MAKECOOKIE)
+
+install-script:
+ $(INSTALL_BIN) $(WORKSRC)/bin/$(GARNAME)
+ $(MAKECOOKIE)
=== added file 'pkg/bio/barrnap/sha256sums'
--- a/pkg/bio/barrnap/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/barrnap/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+3af6cfab0c1c2900fad3651f2e6f24678d522e5487a0366309d0436490dca008
download/barrnap-0.5.tar.gz
=== added directory 'pkg/bio/bedtools'
=== added file 'pkg/bio/bedtools/Makefile'
--- a/pkg/bio/bedtools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bedtools/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = BEDTools
+GARNAME = bedtools
+UPSTREAMNAME = bedtools2
+GARVERSION = 2.22.0
+HOME_URL = https://github.com/arq5x/bedtools2
+DESCRIPTION = A swiss army knife for genome arithmetic
+define BLURB
+bedtools consists of a set of utilities for performing a wide range of
+genomic analysis tasks. They may primarily be used to enable genome
+arithmetic, such as intersecting, merging or complementing genomic
+intervals.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1093/bioinformatics/btq033
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = arq5x/$(UPSTREAMNAME)/archive/
+DISTFILES = v$(GARVERSION).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for f in $(WORKSRC)/bin/*; do \
+ $(INSTALL_BIN) $$f; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/bedtools/sha256sums'
--- a/pkg/bio/bedtools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bedtools/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+d45d37ecfa3f4a5d75dede4df59cd9666d62a34cb38b214741a0adda06075899
download/v2.22.0.tar.gz
=== added directory 'pkg/bio/bfast'
=== added file 'pkg/bio/bfast/Makefile'
--- a/pkg/bio/bfast/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bfast/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,43 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = BFAST
+GARNAME = bfast
+GARVERSION = 0.7.0a
+HOME_URL = http://bfast.sourceforge.net
+DESCRIPTION = Blat-like Fast Accurate Search Tool
+define BLURB
+BFAST is a tool for mapping short reads to reference sequences. Its
+focus is on high-efficiency for mapping billions of reads.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1371/journal.pone.0007767
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/0.7.0/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/bfast/sha256sums'
--- a/pkg/bio/bfast/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bfast/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e
download/bfast-0.7.0a.tar.gz
=== added directory 'pkg/bio/bismark'
=== added file 'pkg/bio/bismark/Makefile'
--- a/pkg/bio/bismark/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bismark/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,56 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Bismark
+GARNAME = bismark
+GARVERSION = 0.10.1
+HOME_URL = http://www.bioinformatics.babraham.ac.uk/projects/bismark/
+DESCRIPTION = A bisulfite read mapper and methylation caller
+define BLURB
+Bismark is a tool to map bisulfate-converted sequence reads and to
+determine cytosine methylation states.
+endef
+LICENSE = GPLv3 or later
+CITE =
+
+######################################################################
+
+MASTER_SITES = http://www.bioinformatics.babraham.ac.uk/
+MASTER_SUBDIR = projects/$(GARNAME)/
+DISTNAME = $(GARNAME)_v$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+INSTALL_SCRIPTS = scripts
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-scripts:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/bismark
+ $(INSTALL_BIN) $(WORKSRC)/bismark2bedGraph
+ $(INSTALL_BIN) $(WORKSRC)/bismark2report
+ $(INSTALL_BIN) $(WORKSRC)/bismark_genome_preparation
+ $(INSTALL_BIN) $(WORKSRC)/bismark_methylation_extractor
+ $(INSTALL_BIN) $(WORKSRC)/coverage2cytosine
+ $(INSTALL_BIN) $(WORKSRC)/deduplicate_bismark
+ $(MAKECOOKIE)
=== added file 'pkg/bio/bismark/sha256sums'
--- a/pkg/bio/bismark/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bismark/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+d4a8f0c559b0fe0dccc50e07159e544482496e81adcfe5627ae1f896c93082a9
download/bismark_v0.10.1.tar.gz
=== added directory 'pkg/bio/bowtie'
=== added file 'pkg/bio/bowtie/Makefile'
--- a/pkg/bio/bowtie/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bowtie/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,59 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Bowtie 2
+GARNAME = bowtie
+UPSTREAMNAME = bowtie2
+GARVERSION = 2.2.4
+HOME_URL = http://bowtie-bio.sourceforge.net/bowtie2
+DESCRIPTION = Fast and sensitive read alignment
+define BLURB
+Bowtie is a fast, memory-efficient tool for aligning short DNA
+sequences (reads) to long reference sequences. It supports gapped,
+local and paired-end alignment modes.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1038/nmeth.1923
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)-bio/files/$(UPSTREAMNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME)-source.zip
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = programs
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-programs:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-align-l
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-align-s
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-build
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-build-l
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-build-s
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-inspect
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-inspect-l
+ $(INSTALL_BIN) $(WORKSRC)/bowtie2-inspect-s
+ $(MAKECOOKIE)
=== added file 'pkg/bio/bowtie/sha256sums'
--- a/pkg/bio/bowtie/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bowtie/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+1f3482bf31111dbfb8b547f984c4755296316f6c48c33c7d3cf19c814785d0aa
download/bowtie2-2.2.4-source.zip
=== added directory 'pkg/bio/breakway'
=== added file 'pkg/bio/breakway/Makefile'
--- a/pkg/bio/breakway/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/breakway/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,68 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Breakway
+GARNAME = breakway
+GARVERSION = 0.7.1
+HOME_URL = http://breakway.sourceforge.net
+DESCRIPTION = Report structural variation breakpoints in genomic data
+define BLURB
+Breakway is a suite of programs that can be used to determine
+structural variation breakpoints in genomic data.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1371/journal.pgen.1000832
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(DISTNAME)/
+DISTNAME = $(GARNAME).$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+INSTALL_SCRIPTS = scripts
+
+BUILDDEPS =
+LIBDEPS = samtools bfast
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+SCRIPTS = $(WORKSRC)/breakway.run.pl \
+ $(WORKSRC)/scripts/breakway.2Dcombine.pl \
+ $(WORKSRC)/scripts/breakway.bwfilter.pl \
+ $(WORKSRC)/scripts/breakway.parameters.pl \
+ $(WORKSRC)/scripts/breakway.readclusters.pl \
+ $(WORKSRC)/scripts/breakway.repeatmasker.pl \
+ $(WORKSRC)/scripts/breakway.segdupfilter.pl \
+ $(WORKSRC)/scripts/breakway.selfchainfilter.pl \
+ $(WORKSRC)/scripts/breakway.sharpenedges.pl
+
+pre-install:
+ for f in $(SCRIPTS); do \
+ sed -i '1s|./usr/bin/perl|/usr/bin/env perl|' $$f; \
+ done
+ $(MAKECOOKIE)
+
+install-scripts:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for f in $(SCRIPTS); do \
+ $(INSTALL_BIN) $$f; \
+ done
+ $(MAKECOOKIE)
+
=== added file 'pkg/bio/breakway/sha256sums'
--- a/pkg/bio/breakway/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/breakway/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+5436c5138a8ed7ae1766970463d5d862ef1897aa81a80d861a8285d6bba58784
download/breakway.0.7.1.tar.gz
=== added directory 'pkg/bio/bwa'
=== added file 'pkg/bio/bwa/Makefile'
--- a/pkg/bio/bwa/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bwa/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,49 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Burrows-Wheeler Aligner
+GARNAME = bwa
+GARVERSION = 0.7.8
+HOME_URL = http://bio-bwa.sourceforge.net/
+DESCRIPTION = Map low-divergent sequences against a large reference genome
+define BLURB
+BWA is a package for mapping low-divergent sequences against a large
+reference genome.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1093/bioinformatics/btp698
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = bio-$(GARNAME)/files/
+DISTFILES = $(DISTNAME).tar.bz2
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/bwa
+ $(MAKECOOKIE)
=== added file 'pkg/bio/bwa/sha256sums'
--- a/pkg/bio/bwa/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bwa/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+6669dbf7486a83acc4453a3c68a7857a76f1c229e229a02a9bae638480fb0b09
download/bwa-0.7.8.tar.bz2
=== added directory 'pkg/bio/cd-hit'
=== added file 'pkg/bio/cd-hit/Makefile'
--- a/pkg/bio/cd-hit/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/cd-hit/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = CD-HIT
+GARNAME = cd-hit
+UPSTREAMNAME = cdhit
+GARVERSION = 4.6.1
+VERSIONDATE = 2012-08-27
+HOME_URL = http://weizhong-lab.ucsd.edu/cd-hit/
+DESCRIPTION = Cluster and compare protein or nucleotide sequences
+define BLURB
+CD-HIT is a program for clustering and comparing protein or nucleotide
+sequences.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1093/bioinformatics/bts565
+
+######################################################################
+
+MASTER_SITES = https://$(UPSTREAMNAME).googlecode.com/
+MASTER_SUBDIR = files/
+DISTNAME = $(GARNAME)-v$(GARVERSION)-$(VERSIONDATE)
+DISTFILES = $(DISTNAME).tgz
+PATCHFILES = $(DISTNAME)-fix-max-sequences.diff
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+INSTALL_ARGS = PREFIX=$(packageprefix)/bin
+
+pre-install:
+ mkdir -p $(packageprefix)/bin
+ $(MAKECOOKIE)
=== added directory 'pkg/bio/cd-hit/files'
=== added file
'pkg/bio/cd-hit/files/cd-hit-v4.6.1-2012-08-27-fix-max-sequences.diff'
--- a/pkg/bio/cd-hit/files/cd-hit-v4.6.1-2012-08-27-fix-max-sequences.diff
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/cd-hit/files/cd-hit-v4.6.1-2012-08-27-fix-max-sequences.diff
2016-06-17 19:57:40 +0000
@@ -0,0 +1,12 @@
+diff -x config.log -x config.status -ru
work/cd-hit-v4.6.1-2012-08-27/cdhit-common.c++
work/cd-hit-v4.6.1-2012-08-27/cdhit-common.c++
+--- work/cd-hit-v4.6.1-2012-08-27/cdhit-common.c++ 2012-08-27
22:09:44.000000000 +0100
++++ work/cd-hit-v4.6.1-2012-08-27/cdhit-common.c++ 2014-07-21
18:10:49.199468558 +0100
+@@ -2288,7 +2288,7 @@
+ double frac = max_sequences / (double) max_entries;
+ max_entries = (options.max_memory - mem_need) /
sizeof(IndexCount);
+ max_sequences = (size_t)(max_entries * frac);
+- if( max_sequences > MAX_TABLE_SEQ ) max_sequences =
MAX_TABLE_SEQ;
++ if( max_sequences > MAX_TABLE_SEQ || max_sequences == 0 )
max_sequences = MAX_TABLE_SEQ;
+ }
+ printf( "Table limit with the given memory limit:\n" );
+ printf( "Max number of representatives: %zu\n", max_sequences );
=== added file 'pkg/bio/cd-hit/sha256sums'
--- a/pkg/bio/cd-hit/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/cd-hit/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,2 @@
+5e26431892609511992542c39705a1427e2fd6a526241977c527dfc74f795932
download/cd-hit-v4.6.1-2012-08-27.tgz
+27ea5519a99522cd04b34ac1bb7615dbd2c6adeaddebb2a85552394045478813
download/cd-hit-v4.6.1-2012-08-27-fix-max-sequences.diff
=== added directory 'pkg/bio/clustal-omega'
=== added file 'pkg/bio/clustal-omega/Makefile'
--- a/pkg/bio/clustal-omega/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/clustal-omega/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,42 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Clustal Omega
+GARNAME = clustal-omega
+GARVERSION = 1.2.1
+HOME_URL = http://www.clustal.org/omega/
+DESCRIPTION = The last alignment program you will ever need
+define BLURB
+Clustal Omega is a multiple sequence alignment tool geared towards
+high-performance and scalability.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1038/msb.2011.75
+
+######################################################################
+
+MASTER_SITES = http://www.clustal.org/
+MASTER_SUBDIR = omega/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = argtable
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/clustal-omega/sha256sums'
--- a/pkg/bio/clustal-omega/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/clustal-omega/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a
download/clustal-omega-1.2.1.tar.gz
=== added directory 'pkg/bio/clustalw'
=== added file 'pkg/bio/clustalw/Makefile'
--- a/pkg/bio/clustalw/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/clustalw/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,42 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Clustal W
+GARNAME = clustalw
+GARVERSION = 2.1
+HOME_URL = http://www.clustal.org/clustal2/
+DESCRIPTION = Multiple alignment of nucleic acid and protein sequences
+define BLURB
+Clustal W is a general purpose multiple alignment program for DNA or
+proteins.
+endef
+LICENSE = LGPL3
+CITE = doi:10.1093/bioinformatics/btm404
+
+######################################################################
+
+MASTER_SITES = http://www.clustal.org/download/
+MASTER_SUBDIR = current/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/clustalw/sha256sums'
--- a/pkg/bio/clustalw/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/clustalw/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486
download/clustalw-2.1.tar.gz
=== added directory 'pkg/bio/csblast'
=== added file 'pkg/bio/csblast/Makefile'
--- a/pkg/bio/csblast/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/csblast/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,79 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = CS-BLAST
+GARNAME = csblast
+GARVERSION = 2.2.4
+HOME_URL = http://toolkit.lmb.uni-muenchen.de/cs_blast
+DESCRIPTION = Context-specific sequence profiels for homology searching
+define BLURB
+CS-BLAST is an extension to NCBI BLAST that improves sensitivity by
+adding context-specific pseudocounts to the input sequence to build
+a profile that more accurately captures the local sequence
+environment.
+endef
+LICENSE = GPLv3+
+CITE = doi:10.1093/bioinformatics/bts622
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = cangermueller/$(GARNAME)/archive/
+DISTFILES = v$(GARVERSION).tar.gz
+# PATCHFILES = $(DISTNAME)-fix-redeclaration.diff \
+# $(DISTNAME)-makefile-modes.diff
+BUILD_SCRIPTS = $(WORKSRC)/src/Makefile $(WORKSRC)/src/Makefile.csalign
+INSTALL_SCRIPTS = bins cslibs
+
+BUILDDEPS =
+LIBDEPS = sparsehash
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+pre-build:
+# The sourcecode for csviz appears to be missing, so don't try to
+# build it.
+ sed -i '/^TARGETS =/s/csviz //' $(WORKSRC)/src/Makefile
+ $(MAKECOOKIE)
+
+build-%/Makefile.csalign:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running make in $(OFF)$*\n"
+ $(BUILD_ENV) $(MAKE) -C $* $(MAKE_ARGS) $(BUILD_ARGS) $(OUTPUT) || \
+ $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-bins:
+ $(INSTALL_BIN) $(WORKSRC)/bin/csblast
+ $(INSTALL_BIN) $(WORKSRC)/bin/csbuild
+ $(INSTALL_BIN) $(WORKSRC)/bin/cscons
+ $(INSTALL_BIN) $(WORKSRC)/bin/cscp_neff
+ $(INSTALL_BIN) $(WORKSRC)/bin/cssgd
+ $(INSTALL_BIN) $(WORKSRC)/bin/cstrainset
+ $(INSTALL_BIN) $(WORKSRC)/bin/cstrainset_neff
+ $(INSTALL_BIN) $(WORKSRC)/bin/cstranslate
+ $(MAKECOOKIE)
+
+install-cslibs:
+ mkdir -p $(packageprefix)/share/$(GARNAME)
+ install -m644 $(WORKSRC)/data/K4000.crf
$(packageprefix)/share/$(GARNAME)/K4000.crf
+ install -m644 $(WORKSRC)/data/K4000.lib
$(packageprefix)/share/$(GARNAME)/K4000.lib
+ install -m644 $(WORKSRC)/data/CS219.lib
$(packageprefix)/share/$(GARNAME)/CS219.lib
+ install -m644 $(WORKSRC)/data/CS62.lib
$(packageprefix)/share/$(GARNAME)/CS62.lib
+ $(MAKECOOKIE)
=== added directory 'pkg/bio/csblast/files'
=== added file 'pkg/bio/csblast/files/csblast-2.2.3-add-missing-targets.diff'
--- a/pkg/bio/csblast/files/csblast-2.2.3-add-missing-targets.diff
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/csblast/files/csblast-2.2.3-add-missing-targets.diff
2016-06-17 19:57:40 +0000
@@ -0,0 +1,28 @@
+diff -x config.log -x config.status -ru tmp/csblast-2.2.3/src/Makefile
work/csblast-2.2.3/src/Makefile
+--- tmp/csblast-2.2.3/src/Makefile 2012-12-12 10:11:10.000000000 +0000
++++ work/csblast-2.2.3/src/Makefile 2014-07-17 14:59:11.988050962 +0100
+@@ -282,6 +282,11 @@
+ cscp_neff: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
++cscp_neff_debug: $(OBJECTS_DEBUG)
++ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
++
++cscp_neff_prof: $(OBJECTS_PROF)
++ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ ### cstrainset_neff ###
+
+@@ -290,6 +295,12 @@
+ cstrainset_neff: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
++cstrainset_neff_debug: $(OBJECTS_DEBUG)
++ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
++
++cstrainset_neff_prof: $(OBJECTS_PROF)
++ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
++
+
+ ### csconvert ###
+
=== added file 'pkg/bio/csblast/files/csblast-2.2.3-fix-redeclaration.diff'
--- a/pkg/bio/csblast/files/csblast-2.2.3-fix-redeclaration.diff
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/csblast/files/csblast-2.2.3-fix-redeclaration.diff
2016-06-17 19:57:40 +0000
@@ -0,0 +1,20 @@
+diff -x config.log -x config.status -ru
work/csblast-2.2.3/src/cstrainset_app.cc
work/csblast-2.2.3/src/cstrainset_app.cc
+--- work/csblast-2.2.3/src/cstrainset_app.cc 2012-12-12 10:11:10.000000000
+0000
++++ work/csblast-2.2.3/src/cstrainset_app.cc 2014-07-17 14:20:59.573573727
+0100
+@@ -434,12 +434,12 @@
+ round = atoi(name.substr(i + 1).c_str());
+ if (round > 0) key = name.substr(0, i); // count-profiles refers to a
specific round
+ }
+- Groups::iterator it = groups.find(key);
+- if (it == groups.end())
++ Groups::iterator it2 = groups.find(key);
++ if (it2 == groups.end())
+ groups[key] = GroupValue(1 << round, round);
+ else {
+- it->second.first |= 1 << round;
+- it->second.second = MAX(it->second.second, round);
++ it2->second.first |= 1 << round;
++ it2->second.second = MAX(it2->second.second, round);
+ }
+ }
+ fprintf(out_, "\n%zu files globbed\n", groups.size());
=== added file 'pkg/bio/csblast/files/csblast-2.2.3-makefile-modes.diff'
--- a/pkg/bio/csblast/files/csblast-2.2.3-makefile-modes.diff 1970-01-01
00:00:00 +0000
+++ b/pkg/bio/csblast/files/csblast-2.2.3-makefile-modes.diff 2016-06-17
19:57:40 +0000
@@ -0,0 +1,291 @@
+diff -x config.log -x config.status -ru work/csblast-2.2.3/src/Makefile
work/csblast-2.2.3/src/Makefile
+--- work/csblast-2.2.3/src/Makefile 2012-12-12 10:11:10.000000000 +0000
++++ work/csblast-2.2.3/src/Makefile 2014-07-17 15:39:06.242278415 +0100
+@@ -1,3 +1,7 @@
++# "debug" for debug mode, "prof" for profiling mode, "test" for test
++# mode
++MODE =
++
+ ### Compiler ###
+
+
+@@ -45,10 +49,10 @@
+
+
+ DEFS = -fno-strict-aliasing \
+- -DVERSION="\"$(VERSION)\"" \
+- -DBUILD_HOST="\"`hostname`\"" \
+- -DBUILD_TIME="\"`date`\"" \
+- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\""
++ -DVERSION="\"$(VERSION)\"" \
++ -DBUILD_HOST="\"`hostname`\"" \
++ -DBUILD_TIME="\"`date`\"" \
++ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\""
+ ifdef LOGGING
+ DEFS += -DLOGGING -DLOG_MAX_LEVEL=$(LOGGING)
+ endif
+@@ -59,15 +63,17 @@
+
+ ### Files ###
+
+-
+-BUILD_DIR = ../build
+-BUILD_DIR_TEST = $(BUILD_DIR)/test
+-BUILD_DIR_PROF = $(BUILD_DIR)/prof
+-BUILD_DIR_DEBUG = $(BUILD_DIR)/debug
++BUILD_ROOT = ../build
++ifeq ($(MODE),test)
++ BUILD_DIR = $(BUILD_ROOT)/test
++else ifeq ($(MODE),debug)
++ BUILD_DIR = $(BUILD_ROOT)/debug
++else ifeq ($(MODE),prof)
++ BUILD_DIR = $(BUILD_ROOT)/prof
++else
++ BUILD_DIR = $(BUILD_ROOT)
++endif
+ $(shell mkdir -p $(BUILD_DIR))
+-$(shell mkdir -p $(BUILD_DIR_TEST))
+-$(shell mkdir -p $(BUILD_DIR_DEBUG))
+-$(shell mkdir -p $(BUILD_DIR_PROF))
+ BIN_DIR = ../bin
+ $(shell mkdir -p $(BIN_DIR))
+ LIB_DIR = ../lib
+@@ -80,10 +86,11 @@
+ DEPS =
+ BASE_DEPS = application aa dna log getopt_pp blosum_matrix assert_helpers
utils
+ GTEST_DEPS = gtest_main gtest-all
+-OBJECTS = $(patsubst %, $(BUILD_DIR)/%.o, $(BASE_DEPS) $(DEPS))
+-OBJECTS_TEST = $(patsubst %, $(BUILD_DIR_TEST)/%.o, $(BASE_DEPS) $(DEPS)
$(GTEST_DEPS))
+-OBJECTS_PROF = $(patsubst %, $(BUILD_DIR_PROF)/%.o, $(BASE_DEPS) $(DEPS))
+-OBJECTS_DEBUG = $(patsubst %, $(BUILD_DIR_DEBUG)/%.o, $(BASE_DEPS) $(DEPS))
++ifeq ($(MODE),test)
++ OBJECTS = $(patsubst %, $(BUILD_DIR)/%.o, $(BASE_DEPS) $(DEPS)
$(GTEST_DEPS))
++else
++ OBJECTS = $(patsubst %, $(BUILD_DIR)/%.o, $(BASE_DEPS) $(DEPS))
++endif
+ INC = -I$$HOME/lib/sparsehash/include
+ LIBS = -lm
+
+@@ -93,13 +100,17 @@
+
+ TARGETS = csblast cstrainset cssgd csbuild csviz csclust cstranslate cscons \
+ cscp_neff cstrainset_neff
cstrainprofiles
+-TARGETS := $(TARGETS) $(TARGETS:%=%_debug) $(TARGETS:%=%_prof)
+ BINS = $(TARGETS:%=$(BIN_DIR)/%)
+
+-PARAMS = $(RELEASE_FLAGS) $(RELEASE_DEFS) $(INC)
+-%_test: PARAMS = $(DEBUG_FLAGS) $(DEBUG_DEFS) $(INC) $(GTEST_FLAGS)
+-%_debug: PARAMS = $(DEBUG_FLAGS) $(DEBUG_DEFS) $(INC)
+-%_prof: PARAMS = $(RELEASE_FLAGS) $(RELEASE_DEFS) $(INC) $(GPROF_FLAGS)
++ifeq ($(MODE),test)
++ PARAMS = $(DEBUG_FLAGS) $(DEBUG_DEFS) $(INC) $(GTEST_FLAGS)
++else ifeq ($(MODE),debug)
++ PARAMS = $(DEBUG_FLAGS) $(DEBUG_DEFS) $(INC)
++else ifeq ($(MODE),prof)
++ PARAMS = $(RELEASE_FLAGS) $(RELEASE_DEFS) $(INC) $(GPROF_FLAGS)
++else
++ PARAMS = $(RELEASE_FLAGS) $(RELEASE_DEFS) $(INC)
++endif
+
+
+ ### Global targets ###
+@@ -110,42 +121,23 @@
+ clean_build:
+ find $(BUILD_DIR) -name '*.o' -exec rm -f '{}' +
+
+-clean_build_test:
+- rm $(BUILD_DIR_TEST)/*.o
+-
+-clean_build_prof:
+- rm $(BUILD_DIR_PROF)/*.o
+-
+-clean_build_debug:
+- rm $(BUILD_DIR_DEBUG)/*.o
+-
+ clean_bin:
+ rm -f $(BINS)
+
+-clean: clean_build clean_build_test clean_build_prof clean_build_debug
cclean_bin
++clean: clean_build clean_bin
+
+ .PHONY: all all_test clean clean_build clean_bin
+
+ $(BUILD_DIR)/%.o: %.$(EXT) $(HEADERS)
+ $(CXX) $(PARAMS) -c -o $@ $<
+
+-$(BUILD_DIR_TEST)/%.o: %.$(EXT) $(HEADERS)
+- $(CXX) $(PARAMS) -c -o $@ $<
+-
+-$(BUILD_DIR_PROF)/%.o: %.$(EXT) $(HEADERS)
+- $(CXX) $(PARAMS) -c -o $@ $<
+-
+-$(BUILD_DIR_DEBUG)/%.o: %.$(EXT) $(HEADERS)
+- $(CXX) $(PARAMS) -c -o $@ $<
+-
+-
+ ### GTEST targets
+
+
+-$(BUILD_DIR_TEST)/gtest-all.o : $(GTEST_SRC)
++$(BUILD_DIR)/gtest-all.o : $(GTEST_SRC)
+ $(CXX) $(PARAMS) -c -o $@ $(GTEST_DIR)/src/gtest-all.cc
+
+-$(BUILD_DIR_TEST)/gtest_main.o : $(GTEST_SRC)
++$(BUILD_DIR)/gtest_main.o : $(GTEST_SRC)
+ $(CXX) $(PARAMS) -c -o $@ $(GTEST_DIR)/src/gtest_main.cc
+
+
+@@ -156,13 +148,6 @@
+ csblast: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-csblast_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-csblast_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-
+ ### cstrainset ###
+
+
+@@ -170,12 +155,6 @@
+ cstrainset: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-cstrainset_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-cstrainset_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### cssgd ###
+
+@@ -184,12 +163,6 @@
+ cssgd: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-cssgd_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-cssgd_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### cshmc ###
+
+@@ -198,12 +171,6 @@
+ cshmc: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-cshmc_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-cshmc_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### csbuild ###
+
+@@ -212,12 +179,6 @@
+ csbuild: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-csbuild_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-csbuild_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### cscons ###
+
+@@ -226,12 +187,6 @@
+ cscons: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-cscons_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-cscons_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### csviz ###
+
+@@ -240,12 +195,6 @@
+ csviz: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-csviz_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-csviz_prof: $(OBJECTS_RPOF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### csclust ###
+
+@@ -254,12 +203,6 @@
+ csclust: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-csclust_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-csclust_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### cstranslate ###
+
+@@ -268,12 +211,6 @@
+ cstranslate: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+-cstranslate_debug: $(OBJECTS_DEBUG)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+-cstranslate_prof: $(OBJECTS_PROF)
+- $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+-
+
+ ### cscp_neff ###
+
+@@ -307,11 +244,11 @@
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = sgd_test
+-sgd_test: $(OBJECTS_TEST)
++sgd_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = crf_test
+-crf_test: $(OBJECTS_TEST)
++crf_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = count_profile_test
+@@ -319,17 +256,17 @@
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = profile_test
+-profile_test: $(OBJECTS_TEST)
++profile_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = library_pseudocounts_test
+-library_pseudocounts_test: $(OBJECTS_TEST)
++library_pseudocounts_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = pseudocounts_test
+-pseudocounts_test: $(OBJECTS_TEST)
++pseudocounts_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
+
+ DEPS = alignment_test blast_hits
+-alignment_test: $(OBJECTS_TEST)
++alignment_test: $(OBJECTS)
+ $(CXX) $(PARAMS) -o $(BIN_DIR)/$(OUTFILE) $+ $(LIBS)
=== added file 'pkg/bio/csblast/sha256sums'
--- a/pkg/bio/csblast/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/csblast/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+76848da4d45a618ae903cafc00ff6387e7decb17b839aca83d9a9438537edf0d
download/v2.2.4.tar.gz
=== added directory 'pkg/bio/cufflinks'
=== added file 'pkg/bio/cufflinks/Makefile'
--- a/pkg/bio/cufflinks/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/cufflinks/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,53 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Cufflinks
+GARNAME = cufflinks
+GARVERSION = 2.1.1
+HOME_URL = http://cufflinks.cbcb.umd.edu/
+DESCRIPTION = Transcript assembly and abundance estimation for RNA-Seq
+define BLURB
+Cufflinks is a tool that assembles transcripts and estimates their
+abundances for RNA-Seq samples. It can be used to test for
+differential expression and regulation.
+endef
+LICENSE = Boost Software License
+CITE = doi:10.1038/nbt.1621
+
+######################################################################
+
+MASTER_SITES = http://cufflinks.cbcb.umd.edu/
+MASTER_SUBDIR = downloads/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = samtools eigen
+
+USE_AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+CONFIGURE_ARGS += --with-bam="$(prefix)" \
+ --with-bam-libdir="$(prefix)/lib" \
+ --with-eigen="$(prefix)/include/eigen3"
+
+pre-configure:
+ sed -i 's|\(EIGEN_CPPFLAGS="-I$$ac_eigen_path\)/include"|\1"|g'
$(WORKSRC)/ax_check_eigen.m4
+ $(MAKECOOKIE)
=== added file 'pkg/bio/cufflinks/sha256sums'
--- a/pkg/bio/cufflinks/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/cufflinks/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+9cbaf1d8f53aa53e6d6beec12420125ee487f9de520417a6b1add3306d01a81e
download/cufflinks-2.1.1.tar.gz
=== added directory 'pkg/bio/dnaa'
=== added file 'pkg/bio/dnaa/Makefile'
--- a/pkg/bio/dnaa/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/dnaa/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,55 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = DNAA
+GARNAME = dnaa
+GARVERSION = 0.1.2
+HOME_URL = http://dnaa.sourceforge.net
+DESCRIPTION = DNA analysis package
+define BLURB
+DNAA is a package of tools for the analysis of short-read next
+generation sequencing data.
+endef
+LICENSE = GPLv2
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = samtools
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+pre-configure:
+ wget -O $(WORKSRC)/bfast-0.7.0a.tar.gz.partial \
+
http://www.sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz
+ mv $(WORKSRC)/bfast-0.7.0a.tar.gz.partial $(WORKSRC)/bfast-0.7.0a.tar.gz
+ gzip -dc $(WORKSRC)/bfast-0.7.0a.tar.gz | tar xf - $(TAR_OPTS) -C
$(WORKSRC)
+ mv $(WORKSRC)/bfast-0.7.0a $(WORKSRC)/bfast
+ wget -O $(WORKSRC)/samtools-0.1.19.tar.bz2.partial \
+
http://www.sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
+ mv $(WORKSRC)/samtools-0.1.19.tar.bz2.partial
$(WORKSRC)/samtools-0.1.19.tar.bz2
+ bzip2 -dc $(WORKSRC)/samtools-0.1.19.tar.bz2 | tar xf - $(TAR_OPTS) -C
$(WORKSRC)
+ mv $(WORKSRC)/samtools-0.1.19 $(WORKSRC)/samtools
+ $(MAKECOOKIE)
=== added file 'pkg/bio/dnaa/sha256sums'
--- a/pkg/bio/dnaa/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/dnaa/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+e6549590066de19e7c5989404830fa3ea82607b864a25147ca16b20a28dd6b68
download/dnaa-0.1.2.tar.gz
=== added directory 'pkg/bio/e-pcr'
=== added file 'pkg/bio/e-pcr/Makefile'
--- a/pkg/bio/e-pcr/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/e-pcr/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,58 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = e-PCR
+GARNAME = e-pcr
+UPSTREAMNAME = e-PCR
+GARVERSION = 2.3.12-1
+HOME_URL = https://www.ncbi.nlm.nih.gov/tools/epcr/
+DESCRIPTION = Electronic PCR
+define BLURB
+e-PCR identifies sequence tagged sites (STS) within DNA sequences,
+allowing you to search for sub-sequences that closely match PCR
+primers.
+endef
+LICENSE = Public Domain
+CITE = PMID:9149949
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.ncbi.nlm.nih.gov/
+MASTER_SUBDIR = pub/schuler/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME)-src.tar.gz
+WORKSRC = $(WORKDIR)/$(subst -1,,$(DISTNAME))
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BUILD_ARGS += links depend all OPTIMIZE=6 prefix=$(prefix)
+INSTALL_ARGS += dirs install
+
+pre-build:
+ sed -i 's/^LDFLAGS =/MYLDFLAGS = $$(LDFLAGS)/'
$(WORKSRC)/stand/config.mk
+ for mf in $(WORKSRC)/stand/Makefile*; do \
+ sed -i 's/$$(LDFLAGS)/$$(MYLDFLAGS)/g' $$mf; \
+ done
+ $(MAKECOOKIE)
+
=== added directory 'pkg/bio/e-pcr/files'
=== added file 'pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff'
--- a/pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff 1970-01-01
00:00:00 +0000
+++ b/pkg/bio/e-pcr/files/e-PCR-2.3.12-include-string_h.diff 2016-06-17
19:57:40 +0000
@@ -0,0 +1,11 @@
+diff -x config.log -x config.status -ru tmp/e-PCR-2.3.12/minilcs.hpp
work/e-PCR-2.3.12/minilcs.hpp
+--- tmp/e-PCR-2.3.12/minilcs.hpp 2009-07-01 15:46:08.000000000 +0100
++++ work/e-PCR-2.3.12/minilcs.hpp 2014-04-08 14:32:07.095577869 +0100
+@@ -34,6 +34,7 @@
+ #include <stdexcept>
+ #include <algorithm>
+ #include <vector>
++#include <string.h>
+
+ #include <ctype.h>
+
=== added file 'pkg/bio/e-pcr/sha256sums'
--- a/pkg/bio/e-pcr/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/e-pcr/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+92613a09cbba3eab66916488063b56e2a3b50a82e5308b1731b6b90d232b8275
download/e-PCR-2.3.12-1-src.tar.gz
=== added directory 'pkg/bio/emboss'
=== added file 'pkg/bio/emboss/Makefile'
--- a/pkg/bio/emboss/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/emboss/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,50 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = EMBOSS
+GARNAME = emboss
+UPSTREAMNAME = EMBOSS
+GARVERSION = 6.6.0
+HOME_URL = http://emboss.sourceforge.net
+DESCRIPTION = A collection of molecular biology packages
+define BLURB
+EMBOSS is a package of programs for use in molecular biology research.
+The programs cover a range of uses, from sequence alignment, to
+protein motif identification, to nucleotide sequence pattern analysis.
+endef
+LICENSE = GPLv2 or later
+CITE = pmid:10827456
+
+######################################################################
+
+MASTER_SITES = ftp://emboss.open-bio.org/
+MASTER_SUBDIR = pub/EMBOSS/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+USE_AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+pre-configure:
+ sed -i
'$$s|$$(bindir)|LD_LIBRARY_PATH=$(packageDESTDIR)$(prefix)/lib:$$LD_LIBRARY_PATH
$$(DESTDIR)$$(bindir)|' $(WORKSRC)/Makefile.am
+ $(MAKECOOKIE)
=== added file 'pkg/bio/emboss/sha256sums'
--- a/pkg/bio/emboss/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/emboss/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e
download/EMBOSS-6.6.0.tar.gz
=== added directory 'pkg/bio/fasttree'
=== added file 'pkg/bio/fasttree/Makefile'
--- a/pkg/bio/fasttree/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fasttree/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,57 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = FastTree
+GARNAME = fasttree
+UPSTREAMNAME = FastTree
+GARVERSION = 2.1.7
+HOME_URL = http://fungi.microbesonline.org/fasttree/
+DESCRIPTION = Fast approximation of maximum-likelihood phylogenetic trees
+define BLURB
+FastTree is a program for the rapid inference of approximately
+maximum-likelihood phylogenetic trees from sequence alignments, using
+relatively low system resources.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1371/journal.pone.0009490
+
+######################################################################
+
+MASTER_SITES = http://fungi.microbesonline.org/
+MASTER_SUBDIR = $(GARNAME)/
+DISTFILES = $(DISTNAME).c
+WORKSRC = $(WORKDIR)
+BUILD_SCRIPTS = program
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+build-program:
+ @printf "[$(OK)build$(OFF)] $(MSG)Building $(NAME) $(OFF)\n"
+ $(CC) -O3 -finline-functions -funroll-loops -Wall -o
$(WORKSRC)/FastTree $(WORKSRC)/$(DISTNAME).c -lm
+ $(MAKECOOKIE)
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME) $(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/FastTree
+ $(MAKECOOKIE)
=== added file 'pkg/bio/fasttree/sha256sums'
--- a/pkg/bio/fasttree/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fasttree/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0
download/FastTree-2.1.7.c
=== added directory 'pkg/bio/fastx-toolkit'
=== added file 'pkg/bio/fastx-toolkit/Makefile'
--- a/pkg/bio/fastx-toolkit/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fastx-toolkit/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = FASTX-Toolkit
+GARNAME = fastx-toolkit
+UPSTREAMNAME = fastx_toolkit
+GARVERSION = 0.0.14
+HOME_URL = http://hannonlab.cshl.edu/fastx_toolkit/
+DESCRIPTION = FASTQ/A short-reads pre-processing tools
+define BLURB
+FASTX-Toolkit is a collection of tools for pre-processing short reads
+in FASTA/FASTQ format before mapping them to a reference genome.
+Their functionality includes filetype conversion, producing quality
+statistics, collapsing identical sequences, or splitting files.
+endef
+LICENSE = AGPL3 or later
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = agordon/$(UPSTREAMNAME)/releases/download/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.bz2
+
+BUILDDEPS =
+LIBDEPS = libgtextutils
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/fastx-toolkit/sha256sums'
--- a/pkg/bio/fastx-toolkit/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fastx-toolkit/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806
download/fastx_toolkit-0.0.14.tar.bz2
=== added directory 'pkg/bio/fsa'
=== added file 'pkg/bio/fsa/Makefile'
--- a/pkg/bio/fsa/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fsa/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = FSA
+GARNAME = fsa
+GARVERSION = 1.15.9
+HOME_URL = http://fsa.sourceforge.net/
+DESCRIPTION = Fast statistical alignment
+define BLURB
+FSA performs sequence alignments in a probabilistic manner via a
+distance-based approach, similar to distance-based phylogenetic
+reconstruction methods. It builds multiple alignments of homologous
+protein, RNA or DNA sequences using only pairwise estimations of
+homology.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1371/journal.pcbi.1000392
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/fsa/sha256sums'
--- a/pkg/bio/fsa/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/fsa/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+6ee6e238e168ccba0d51648ba64d518cdf68fa875061e0d954edfb2500b50b30
download/fsa-1.15.9.tar.gz
=== added directory 'pkg/bio/hmmer'
=== added file 'pkg/bio/hmmer/Makefile'
--- a/pkg/bio/hmmer/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/hmmer/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = HMMR
+GARNAME = hmmer
+GARVERSION = 3.1b1
+HOME_URL = http://hmmer.janelia.org/
+DESCRIPTION = Biosequence analysis using profile hidden Markov models
+define BLURB
+HMMER is used for searching sequence databases for homologs of protein
+sequences, and for making protein sequence alignments. It implements
+methods using probabilistic models called profile hidden Markov models
+(profile HMMs).
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1371/journal.pcbi.1002195
+
+######################################################################
+
+MASTER_SITES = http://selab.janelia.org/software/
+MASTER_SUBDIR = hmmer3/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/hmmer/sha256sums'
--- a/pkg/bio/hmmer/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/hmmer/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+246f5e32545d3a5706d065d8413fc8fc5445e779a97019e98ba319e5ef9dc1d8
download/hmmer-3.1b1.tar.gz
=== added directory 'pkg/bio/hyphy'
=== added file 'pkg/bio/hyphy/Makefile'
--- a/pkg/bio/hyphy/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/hyphy/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,43 @@
+# Copyright © 2013, 2014, 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = HyPhy
+GARNAME = hyphy
+GARVERSION = 2.2.6
+HOME_URL = http://www.hyphy.org
+DESCRIPTION = Hypothesis testing using Phylogenies
+define BLURB
+Hypothesis testing using Phylogenies
+endef
+LICENSE = Expat
+CITE = doi:10.1093/bioinformatics/bti079
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = veg/$(GARNAME)/archive/
+DISTFILES = $(GARVERSION).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
+
+CMAKE_CONFIGURE_ARGS += -DINSTALL_PREFIX=$(prefix)
=== added file 'pkg/bio/hyphy/sha256sums'
--- a/pkg/bio/hyphy/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/hyphy/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+49155a3cb91efc635c9643e0c802111443b597db735c50b0eb61716f13302302
download/2.2.6.tar.gz
=== added directory 'pkg/bio/infernal'
=== added file 'pkg/bio/infernal/Makefile'
--- a/pkg/bio/infernal/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/infernal/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,42 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Infernal
+GARNAME = infernal
+GARVERSION = 1.1.1
+HOME_URL = http://infernal.janelia.org/
+DESCRIPTION = Inference of RNA alignments
+define BLURB
+Infernal is a tool for searching DNA sequence databases for RNA
+structure and sequence similarities.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1093/bioinformatics/btt509
+
+######################################################################
+
+MASTER_SITES = http://selab.janelia.org/
+MASTER_SUBDIR = software/$(GARNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/infernal/sha256sums'
--- a/pkg/bio/infernal/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/infernal/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+9f18ed3ce5ba738db268521c2ac9781449855687016dd50cfcb7fb479a5e319a
download/infernal-1.1.1.tar.gz
=== added directory 'pkg/bio/jellyfish'
=== added file 'pkg/bio/jellyfish/Makefile'
--- a/pkg/bio/jellyfish/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/jellyfish/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,41 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Jellyfish
+GARNAME = jellyfish
+GARVERSION = 2.1.4
+HOME_URL = http://www.genome.umd.edu/jellyfish.html
+DESCRIPTION = Fast, parallel k-mer counting for DNA
+define BLURB
+Jellyfish is a tool for efficient counting of k-mers in DNA sequences.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1093/bioinformatics/btr011
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.genome.umd.edu/pub/
+MASTER_SUBDIR = $(GARNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/jellyfish/sha256sums'
--- a/pkg/bio/jellyfish/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/jellyfish/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+c4e692170d33efa9e6e4f0b134d8e257fb802832af17fdc53ac468bf8f0f29a5
download/jellyfish-2.1.4.tar.gz
=== added directory 'pkg/bio/kraken'
=== added file 'pkg/bio/kraken/Makefile'
--- a/pkg/bio/kraken/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/kraken/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,59 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Kraken
+GARNAME = kraken
+GARVERSION = 0.10.4
+HOME_URL = http://ccb.jhu.edu/software/kraken/
+DESCRIPTION = Taxonomic sequence classification system
+define BLURB
+Kraken is a system for assigning taxonomic labels to short DNA
+sequences, usually obtained through metagenomic studies. It operates
+by utilizing exact alignments of k-mers and a classification
+algorithm.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1186/gb-2014-15-3-r46
+
+######################################################################
+
+MASTER_SITES = http://ccb.jhu.edu/software/
+MASTER_SUBDIR = $(GARNAME)/dl/
+DISTNAME = $(GARNAME)-$(GARVERSION)-beta
+DISTFILES = $(DISTNAME).tgz
+BUILD_SCRIPTS = $(WORKSRC)/src/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/src/Makefile scripts
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+INSTALL_ARGS += KRAKEN_DIR=$(packageprefix)/bin
+
+pre-install:
+ mkdir -p $(packageprefix)/bin
+ $(MAKECOOKIE)
+
+install-scripts:
+ for f in $(WORKSRC)/scripts/*; do \
+ $(INSTALL_BIN) $$f; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/kraken/sha256sums'
--- a/pkg/bio/kraken/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/kraken/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+f4ef264df3564957e508d39c6107244bce6ec0fcdb4b071e035ca7f802a92ee1
download/kraken-0.10.4-beta.tgz
=== added directory 'pkg/bio/macs'
=== added file 'pkg/bio/macs/Makefile'
--- a/pkg/bio/macs/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/macs/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MACS
+GARNAME = macs
+UPSTREAMNAME = MACS
+GARVERSION = 1.4.2
+HOME_URL = http://liulab.dfci.harvard.edu/MACS/
+DESCRIPTION = Model-based analysis for ChIP-Seq
+define BLURB
+MACS is a program for predicting protein-DNA interactions from ChIP-
+Seq data. It works via a model-based analysis that empirically models
+the length of the sequence fragments in order to improve the spatial
+resolution of predicted binding sites.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1186/gb-2008-9-9-r137
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = downloads/taoliu/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/bio/macs/sha256sums'
--- a/pkg/bio/macs/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/macs/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+37788f88d07473e28ddcbf0a29fead48c7556415bf4df7b6bee479ea7ec334f4
download/MACS-1.4.2.tar.gz
=== added directory 'pkg/bio/mafft'
=== added file 'pkg/bio/mafft/Makefile'
--- a/pkg/bio/mafft/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mafft/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,72 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MAFFT
+GARNAME = mafft
+GARVERSION = 7.205
+HOME_URL = http://mafft.cbrc.jp/alignment/software/
+DESCRIPTION = A multiple sequence alignment program
+define BLURB
+MAFFT is a multiple sequence alignment program offering a variety of
+different alignment methods.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1093/molbev/mst010
+
+######################################################################
+
+MASTER_SITES = http://mafft.cbrc.jp/
+MASTER_SUBDIR = alignment/software/
+DISTNAME = $(GARNAME)-$(GARVERSION)-without-extensions
+DISTFILES = $(DISTNAME)-src.tgz
+# PATCHFILES = $(GARNAME)-$(GARVERSION)-destdir-install.patch
+WORKSRC = $(WORKDIR)/$(DISTNAME)/core
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile symlinks
+
+BUILDDEPS =
+LIBDEPS =
+
+PATCHOPTS = -p3
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+INSTALL_ARGS += PREFIX=$(packageprefix)
+LINKED_PROGS = linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi \
+mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi \
+mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi
+
+pre-build:
+ sed -i 's|s:_LIBDIR:$$(LIBDIR)|s:_LIBDIR:$(packagedir)/libexec/mafft|'
$(WORKSRC)/Makefile
+ sed -i 's|s:_BINDIR:$$(BINDIR)|s:_BINDIR:$(packagedir)/bin|'
$(WORKSRC)/Makefile
+ $(MAKECOOKIE)
+
+install-symlinks: install-$(WORKSRC)/Makefile
+ for f in $(LINKED_PROGS); do \
+ rm -f $(packageprefix)/bin/$$f; \
+ ln -s $(packagedir)/bin/mafft $(packageprefix)/bin/$$f; \
+ done
+ rm -f $(packageprefix)/bin/mafft-profile
+ rm -f $(packageprefix)/bin/mafft-profile.exe
+ ln -s $(packagedir)/libexec/mafft-profile
$(packageprefix)/bin/mafft-profile
+ rm -f $(packageprefix)/bin/mafft-distance
+ rm -f $(packageprefix)/bin/mafft-distance.exe
+ ln -s $(packagedir)/libexec/mafft-distance
$(packageprefix)/bin/mafft-distance
+ $(MAKECOOKIE)
=== added file 'pkg/bio/mafft/sha256sums'
--- a/pkg/bio/mafft/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mafft/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+8c114d22b69be0e15ffcf3e4337d9333c6c4523b9c5903b88a893efd0d7f9400
download/mafft-7.205-without-extensions-src.tgz
=== added directory 'pkg/bio/melting'
=== added file 'pkg/bio/melting/Makefile'
--- a/pkg/bio/melting/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/melting/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,64 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MELTING
+GARNAME = melting
+UPSTREAMNAME = MELTING
+GARVERSION = 5.2.0
+HOME_URL = http://www.gnu.org/software/melting/
+DESCRIPTION = Temperature computations for a nucleic acid duplex
+define BLURB
+GNU MELTING computes the enthalpy, entropy and melting temperature of
+helix-coil transitions of a nucleic acid duplex.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1186/1471-2105-13-101.
+
+######################################################################
+
+DISTNAME = $(UPSTREAMNAME)$(GARVERSION)
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/meltingJava/melting5/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+BUILD_SCRIPTS = $(WORKSRC)/buildProject.sh
+INSTALL_SCRIPTS = all
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+build-%/buildProject.sh:
+ @echo -e "[$(OK)build$(OFF)] $(MSG)Running buildProject.sh in
$*\n$(OFF)"
+ cd $* && ./buildProject.sh
+ $(MAKECOOKIE)
+
+install-all:
+ @echo -e "[$(OK)install$(OFF)] $(MSG)Manually installing all$(OFF)"
+ @mkdir -p $(packageprefix)
+ @mkdir -p $(packageprefix)/bin
+ @mkdir -p $(packageprefix)/$(UPSTREAMNAME)/src
+ @install -m755 -D $(WORKSRC)/executable/melting
$(packageprefix)/bin/melting
+ @install -m755 -D $(WORKSRC)/executable/melting5.jar
$(packageprefix)/bin/melting5.jar
+ @for f in $(WORKSRC)/Data/*; do \
+ install -m644 $$f $(packageprefix)/$(UPSTREAMNAME)/src/`$$f`; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/melting/sha256sums'
--- a/pkg/bio/melting/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/melting/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+a3633c8f74ce383bbc3a339f99081a76c6529c10d9bdff1ad91b63e6d919a7bb
download/MELTING5.2.0.tar.gz
=== added directory 'pkg/bio/minced'
=== added file 'pkg/bio/minced/Makefile'
--- a/pkg/bio/minced/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/minced/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,55 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MinCED
+GARNAME = minced
+GARVERSION = 0.1.6
+HOME_URL = https://github.com/ctSkennerton/minced
+DESCRIPTION = Mine CRISPRs in environmental datasets
+define BLURB
+MinCED predicts Clustered Regularly Interspaced Short Palindromic
+Repeats (CRISPRs) in genomes or metagenomes.
+endef
+LICENSE = GPLv3
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = ctSkennerton/$(GARNAME)/archive/
+DISTFILES = $(GARVERSION).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = library bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-library:
+ install -d $(packageprefix)/share/$(GARNAME)
+ install -m644 $(WORKSRC)/minced.jar
$(packageprefix)/share/$(GARNAME)/minced.jar
+ $(MAKECOOKIE)
+
+install-bin:
+ install -d $(packageprefix)/bin
+ printf '#!/bin/sh\njava -jar $(prefix)/share/$(GARNAME)/minced.jar
"$$@"' >$(WORKSRC)/minced
+ $(INSTALL_BIN) $(WORKSRC)/minced
+ $(MAKECOOKIE)
=== added file 'pkg/bio/minced/sha256sums'
--- a/pkg/bio/minced/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/minced/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+035e343591b4595c571e17b0b3f526a01a23c3a47ebafb66f20ba667b29b3ed7
download/0.1.6.tar.gz
=== added directory 'pkg/bio/moods'
=== added file 'pkg/bio/moods/Makefile'
--- a/pkg/bio/moods/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/moods/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,60 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MOODS
+GARNAME = moods
+UPSTREAMNAME = MOODS
+GARVERSION = 1.0.2
+HOME_URL = http://www.cs.helsinki.fi/group/pssmfind/
+DESCRIPTION = Motif occurrence detection suite
+define BLURB
+MOODS is a library containing algorithms for matching position weight
+matrices (PWM) against DNA sequences.
+endef
+LICENSE = GPL3
+CITE = doi:10.1093/bioinformatics/btp554
+
+######################################################################
+
+MASTER_SITES = http://www.cs.helsinki.fi/
+MASTER_SUBDIR = group/pssmfind/
+DISTNAME = $(UPSTREAMNAME)_$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(UPSTREAMNAME)
+CONFIGURE_SCRIPTS = $(WORKSRC)/perl/Makefile.PL
+BUILD_SCRIPTS = $(WORKSRC)/src/Makefile $(WORKSRC)/python/setup.py \
+ $(WORKSRC)/perl/Makefile
+INSTALL_SCRIPTS = bin lib $(WORKSRC)/python/setup.py \
+ $(WORKSRC)/perl/Makefile
+
+BUILDDEPS =
+LIBDEPS = python2
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bin:
+ $(INSTALL_BIN) $(WORKSRC)/src/find_pssm_dna
+ $(MAKECOOKIE)
+
+install-lib:
+ $(INSTALL_LIB) $(WORKSRC)/src/libpssm.a
+ $(MAKECOOKIE)
=== added file 'pkg/bio/moods/sha256sums'
--- a/pkg/bio/moods/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/moods/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+a3bf43a6e0ef5d48fc85e3246021b7b007e52648405fd187aeaa712d2dbf3dfd
download/MOODS_1.0.2.tar.gz
=== added directory 'pkg/bio/mrbayes'
=== added file 'pkg/bio/mrbayes/Makefile'
--- a/pkg/bio/mrbayes/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mrbayes/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,59 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MrBayes
+GARNAME = mrbayes
+GARVERSION = 3.2.3
+HOME_URL = http://mrbayes.sourceforge.net/
+DESCRIPTION = Bayesian inference of phylogeny
+define BLURB
+MrBayes is a program for the inference of phylogenies and model choice
+that uses Markov chain Monte Carlo methods to estimate the posterior
+distribution of model parameters. It supports a range of phylogenetic
+and evolutionary models.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1093/sysbio/sys029
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+EXTRACTDIR = $(WORKDIR)/$(GARNAME)_$(GARVERSION)
+WORKSRC = $(EXTRACTDIR)/src
+
+BUILDDEPS =
+LIBDEPS = beagle-lib
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+CONFIGURE_ARGS += --with-beagle="$(prefix)"
+
+pre-configure:
+ cd $(WORKSRC) && autoconf
+ sed -i 's|^BINDIR *=.*|BINDIR = $(prefix)/bin|' $(WORKSRC)/Makefile.in
+ sed -i 's|$$(BINDIR)|$$(DESTDIR)$$(BINDIR)/mb|' $(WORKSRC)/Makefile.in
+ $(MAKECOOKIE)
+
+pre-install:
+ install -d $(packageprefix)/bin
+ $(MAKECOOKIE)
+
=== added file 'pkg/bio/mrbayes/sha256sums'
--- a/pkg/bio/mrbayes/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mrbayes/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+b16e7f8517a51a7954e184d32890c28a12133101eff18d74c3d86392c23a3330
download/mrbayes-3.2.3.tar.gz
=== added directory 'pkg/bio/mummer'
=== added file 'pkg/bio/mummer/Makefile'
--- a/pkg/bio/mummer/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mummer/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,59 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = MUMmer
+GARNAME = mummer
+UPSTREAMNAME = MUMmer
+GARVERSION = 3.23
+HOME_URL = http://mummer.sourceforge.net/
+DESCRIPTION = Ultra-fast alignment of large-scale sequences
+define BLURB
+MUMmer is a system for rapidly aligning entire genomes from the
+nucleotide sequence or, if the species are too divergent, from the
+translations of the input sequences.
+endef
+LICENSE = Aritistic License
+CITE = PMID:14759262
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+DISTNAME = $(UPSTREAMNAME)$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BINS = annotate combineMUMs delta-filter dnadiff exact-tandems gaps \
+ mapview mgaps mummer mummerplot nucmer nucmer2xfig promer
\
+ repeat-match run-mummer1 run-mummer3 show-aligns show-coords \
+ show-diff show-snps show-tiling
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for bin in $(BINS); do \
+ $(INSTALL_BIN) $(WORKSRC)/$$bin; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/mummer/sha256sums'
--- a/pkg/bio/mummer/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/mummer/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
download/MUMmer3.23.tar.gz
=== added directory 'pkg/bio/ncbi-blast'
=== added file 'pkg/bio/ncbi-blast/Makefile'
--- a/pkg/bio/ncbi-blast/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/ncbi-blast/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,59 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = BLAST+
+GARNAME = ncbi-blast
+GARVERSION = 2.2.30
+HOME_URL = http://blast.ncbi.nlm.nih.gov
+DESCRIPTION = Basic Local Alignment Search Tool
+define BLURB
+BLAST+ is a sequence similarity search program. It can be used to search a
+sequence database for regions of similarity to the query sequence.
+endef
+LICENSE = Public Domain
+CITE = doi:10.1186/1471-2105-10-421.
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.ncbi.nlm.nih.gov/
+MASTER_SUBDIR = blast/executables/blast+/$(GARVERSION)/
+DISTNAME = $(GARNAME)-$(GARVERSION)+-src
+DISTFILES = $(DISTNAME).tar.gz
+#PATCHFILES = $(DISTNAME)-include-typeinfo.diff
+WORKSRC = $(WORKDIR)/$(DISTNAME)/c++
+
+BUILDDEPS =
+LIBDEPS =
+
+PATCHOPTS = -p3
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+pre-install:
+ sed -i 's/$$(bindir)/$$(DESTDIR)$$(bindir)/g' $(WORKSRC)/Makefile
+ sed -i 's/$$(libdir)/$$(DESTDIR)$$(libdir)/g' $(WORKSRC)/Makefile
+ sed -i 's/$$(pincludedir)/$$(DESTDIR)$$(pincludedir)/g'
$(WORKSRC)/Makefile
+ sed -i 's/$$(exec_prefix)/$$(DESTDIR)$$(exec_prefix)/g'
$(WORKSRC)/Makefile
+ sed -i '47,50d' $(WORKSRC)/Makefile
+ $(MAKECOOKIE)
+
+post-install:
+ cd $(packagedir)/lib && for x in *.a; do ln -s "$$x" "`basename \"$$x\"
.a`-static.a"; done
+ $(MAKECOOKIE)
=== added directory 'pkg/bio/ncbi-blast/files'
=== added file
'pkg/bio/ncbi-blast/files/ncbi-blast-2.2.29+-src-include-typeinfo.diff'
--- a/pkg/bio/ncbi-blast/files/ncbi-blast-2.2.29+-src-include-typeinfo.diff
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/ncbi-blast/files/ncbi-blast-2.2.29+-src-include-typeinfo.diff
2016-06-17 19:57:40 +0000
@@ -0,0 +1,11 @@
+diff -x config.log -x config.status -ru
work/ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp
work/ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp
+--- work/ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp
2013-09-06 19:29:54.000000000 +0100
++++ work/ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp
2014-06-06 12:19:33.273697088 +0100
+@@ -35,6 +35,7 @@
+ /// The NCBI C++/STL use hints.
+
+
++#include <typeinfo>
+ #include <common/ncbi_export.h>
+ #include <string>
+
=== added file 'pkg/bio/ncbi-blast/sha256sums'
--- a/pkg/bio/ncbi-blast/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/ncbi-blast/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40
download/ncbi-blast-2.2.30+-src.tar.gz
=== added directory 'pkg/bio/ncbi-tools'
=== added file 'pkg/bio/ncbi-tools/Makefile'
--- a/pkg/bio/ncbi-tools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/ncbi-tools/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,78 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = NCBI Software Development Toolkit
+GARNAME = ncbi-tools
+GARVERSION = 2012-02-12
+HOME_URL = ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm
+DESCRIPTION = A toolkit for the development of NCBI services
+define BLURB
+The NCBI Software Development Toolkit is a general collection of code
+used in developing various NCBI services. It also includes some
+demo tools that are useful in their own right, such as file-format
+convertors.
+endef
+LICENSE = Public Domain
+CITE =
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.ncbi.nih.gov/
+MASTER_SUBDIR = toolbox/ncbi_tools/
+DISTFILES = ncbi.tar.gz
+EXTRACTDIR = $(WORKDIR)/$(DISTNAME)
+WORKSRC = $(EXTRACTDIR)
+BUILD_SCRIPTS = $(WORKSRC)/ncbi/make/makedis.csh
+INSTALL_SCRIPTS = bins mans
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BINS = errhdr testobj checksub blastcl3 entrcmd megablast fa2htgs
\
+copymat ln-if-absent indexpub gil2bin testval blastpgp getpub impala \
+wblast2_cs.REAL macro.asn valapi.c cdscan blastclust tblfix.pl
\
+vecscreen asn2gb asndhuff idfetch testcore taxblast seedtop
\
+macroapi.c debruijn asn2idx sortbyquote subfuse rpsblast demo_regexp \
+test_regexp fastacmd bl2bag.cgi formatdb valdlg.c dosimple asn2ff
\
+wblast2.REAL sqnutil4.c gbf2tbl.pl makemat nph-viewgif.cgi ncbisort
\
+makeset formatrpsdb bl2seq getmesh seqtest macrodlg.c test_regexp.sh \
+objmacro.c tbl2asn asn2xml blastall demo_regexp_grep findspl gene2xml \
+asntool
+
+build-%/makedis.csh:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running make in $(OFF)$*\n"
+ cd $(WORKSRC) && ./ncbi/make/makedis.csh 2>&1 | tee out.makedis.txt
+ $(MAKECOOKIE)
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing binaries $(OFF)\n"
+ for bin in $(BINS); do \
+ $(INSTALL_BIN) $(WORKSRC)/ncbi/build/$$bin; \
+ done
+ $(MAKECOOKIE)
+
+install-mans:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing manfiles $(OFF)\n"
+ for bin in $(BINS); do \
+ test -f $(WORKSRC)/ncbi/doc/man/$$bin.1 && $(INSTALL_MAN)
$(WORKSRC)/ncbi/doc/man/$$bin.1; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/ncbi-tools/sha256sums'
--- a/pkg/bio/ncbi-tools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/ncbi-tools/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d
download/ncbi.tar.gz
=== added directory 'pkg/bio/newick-utils'
=== added file 'pkg/bio/newick-utils/Makefile'
--- a/pkg/bio/newick-utils/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/newick-utils/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,48 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = The Newick Utilities
+GARNAME = newick-utils
+GARVERSION = 1.6
+HOME_URL = http://cegg.unige.ch/newick_utils
+DESCRIPTION = Command-line tools for processing phylogenetic trees
+define BLURB
+The Newick Utilities are a suite of command-line tools for processing
+phylogenetic trees. Their functionality includes re-rooting,
+extracting subtrees, trimming, pruning, condensing and drawing.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1093/bioinformatics/btq243
+
+######################################################################
+
+MASTER_SITES = http://cegg.unige.ch/
+MASTER_SUBDIR = pub/
+DISTFILES = $(DISTNAME).tar.gz
+ifeq ($(shell lua -v | grep -q "5.2" && echo yes),yes)
+ PATCHFILES = $(DISTNAME)-compile-w-lua-5.2.patch
+endif
+
+BUILDDEPS =
+LIBDEPS =
+
+AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added directory 'pkg/bio/newick-utils/files'
=== added file
'pkg/bio/newick-utils/files/newick-utils-1.6-compile-w-lua-5.2.patch'
--- a/pkg/bio/newick-utils/files/newick-utils-1.6-compile-w-lua-5.2.patch
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/newick-utils/files/newick-utils-1.6-compile-w-lua-5.2.patch
2016-06-17 19:57:40 +0000
@@ -0,0 +1,145 @@
+:100755 100755 e5efd15... 47eee1a... M src/lua_tree_editor.c
+
+diff --git work/newick-utils-1.6/src/lua_tree_editor.c
work/newick-utils-1.6/src/lua_tree_editor.c
+index e5efd15..47eee1a 100755
+--- work/newick-utils-1.6/src/lua_tree_editor.c
++++ work/newick-utils-1.6/src/lua_tree_editor.c
+@@ -613,6 +613,33 @@ static void set_predefined_variables(struct rnode *node,
lua_State *L)
+ assert(lua_gettop(L) == initial_lua_stack_size);
+ }
+
++/* Pushes onto the stack the function at index '*phase' in the globals table.
*/
++// TODO: try lua_getglobal!!!
++
++static void get_user_hook(lua_State *L, const char *phase)
++{
++ const lua_Number *version = lua_version(L);
++ lua_rawgeti(L, LUA_REGISTRYINDEX, LUA_RIDX_GLOBALS);
++ lua_getfield(L, -1, NODE);
++ //lua_getfield(L, LUA_GLOBALSINDEX, NODE);
++}
++
++/* Sets the element at index '*phase' in the globals table to the hook
function
++ * at the top of the stack. */
++
++static void set_user_hook(lua_State *L, const char *phase)
++{
++ /* hook is at -1 */
++ const lua_Number *version = lua_version(L);
++ lua_rawgeti(L, LUA_REGISTRYINDEX, LUA_RIDX_GLOBALS);
++ /* hook at -2, globals table at -1 */
++ lua_insert(L, -2);
++ /* globals at -2, hook at -1 */
++ lua_setfield(L, -2, NODE);
++ //lua_getfield(L, LUA_GLOBALSINDEX, NODE);
++}
++
++
+ static void process_tree(struct rooted_tree *tree, lua_State *L,
+ struct parameters params)
+ {
+@@ -649,7 +676,7 @@ static void process_tree(struct rooted_tree *tree,
lua_State *L,
+ }
+
+ set_predefined_variables(current_node, L);
+- lua_getfield(L, LUA_GLOBALSINDEX, NODE);
++ lua_getglobal(L, NODE);
+ lua_call(L, 0, 0);
+ } /* loop over all nodes */
+
+@@ -756,7 +783,7 @@ static void load_lua_condition(lua_State * L, char
*lua_condition)
+ printf("%s\n", msg);
+ exit(EXIT_FAILURE);
+ }
+- lua_setfield(L, LUA_GLOBALSINDEX, CONDITION);
++ lua_setglobal(L, CONDITION);
+ }
+
+ static void load_lua_action(lua_State *L, char *lua_action)
+@@ -768,7 +795,7 @@ static void load_lua_action(lua_State *L, char *lua_action)
+ printf("%s\n", msg);
+ exit(EXIT_FAILURE);
+ }
+- lua_setfield(L, LUA_GLOBALSINDEX, ACTION);
++ lua_setglobal(L, ACTION);
+ }
+
+ static void run_user_hooks_file(lua_State * L, char *user_hooks_filename)
+@@ -927,7 +954,7 @@ static int lua_cli_process_node(lua_State *L)
+ if (NULL == lnode)
+ luaL_error(L, "N is not a node");
+
+- lua_getfield(L, LUA_GLOBALSINDEX, CONDITION);
++ lua_getglobal(L, CONDITION);
+ lua_call(L, 0, 1);
+ if (lua_isboolean(L, -1) != 1) {
+ fprintf(stderr, "WARNING: condition does not evaluate "
+@@ -938,10 +965,10 @@ static int lua_cli_process_node(lua_State *L)
+ int match = lua_toboolean(L, -1);
+ lua_pop(L, 1);
+ if (match) {
+- lua_getfield(L, LUA_GLOBALSINDEX, ACTION);
++ lua_getglobal(L, ACTION);
+ lua_call(L, 0, 0);
+ /* see -o switch */
+- lua_getfield(L, LUA_GLOBALSINDEX, STOP_AT_1ST_MATCH);
++ lua_getglobal(L, STOP_AT_1ST_MATCH);
+ int stop_clade_at_first_match = lua_toboolean(L, -1);
+ lua_pop(L, 1);
+ if (stop_clade_at_first_match)
+@@ -953,7 +980,7 @@ static int lua_cli_process_node(lua_State *L)
+ // TODO: implement __tostring for lua_rnode
+
+ /* Functions for Lua node */
+-static const struct luaL_reg lnodelib_f [] = {
++static const struct luaL_Reg lnodelib_f [] = {
+ {"set", lua_node_set},
+ {"get", lua_node_get},
+ {NULL, NULL}
+@@ -979,9 +1006,10 @@ static int luaopen_lnode (lua_State *L)
+ return 0;
+ }
+
++
+ static void run_user_hook(lua_State *L, const char *phase)
+ {
+- lua_getfield(L, LUA_GLOBALSINDEX, phase);
++ lua_getglobal(L, phase);
+ // TODO: this lua_isfunction() check should be done once and for all,
+ // before the tree is processed, like for the NODE function (see main(),
+ // around l. 956
+@@ -997,7 +1025,7 @@ int main(int argc, char* argv[])
+ struct rooted_tree *tree;
+
+ /* Initializes Lua */
+- lua_State *L = lua_open();
++ lua_State *L = luaL_newstate();
+ luaL_openlibs(L);
+
+ lua_pushcfunction(L, lua_print_subclade);
+@@ -1017,8 +1045,9 @@ int main(int argc, char* argv[])
+ }
+
+ if (NULL != params.user_hooks_filename) {
++ /* Get the node() function defined by the user */
+ run_user_hooks_file(L, params.user_hooks_filename);
+- lua_getfield(L, LUA_GLOBALSINDEX, NODE);
++ lua_getglobal(L, NODE);
+ int NODE_type = lua_type(L, -1);
+ switch(NODE_type) {
+ case LUA_TFUNCTION:
+:100755 100755 4aefb5a... ecdc57b... M configure.ac
+
+diff --git work/newick-utils-1.6/configure.ac
work/newick-utils-1.6/configure.ac
+index 4aefb5a..ecdc57b 100755
+--- work/newick-utils-1.6/configure.ac
++++ work/newick-utils-1.6/configure.ac
+@@ -95,7 +95,7 @@ AS_IF([test "x$with_lua" = xyes],
+ AM_CPPFLAGS="$AM_CPPFLAGS $CPPFLAGS"
+ AC_CHECK_HEADERS([lua.h], [], [with_lua=no_hdr])
+ AM_CPPFLAGS="$OLD_AM_CPPFLAGS"
+- AC_SEARCH_LIBS([luaL_openlibs], [lua5.1 lua-5.1 lua],
++ AC_SEARCH_LIBS([luaL_openlibs], [lua5.2 lua-5.2.1 lua],
+ [], [with_lua=no_lib])
+ ]
+ )
=== added file 'pkg/bio/newick-utils/sha256sums'
--- a/pkg/bio/newick-utils/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/newick-utils/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+2c142a2806f6e1598585c8be5afba6d448c572ad21c142e70d6fd61877fee798
download/newick-utils-1.6.tar.gz
=== added directory 'pkg/bio/oma'
=== added file 'pkg/bio/oma/Makefile'
--- a/pkg/bio/oma/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/oma/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,97 @@
+# Copyright © 2014, 2015, 2016 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = OMA
+GARNAME = oma
+GARVERSION = 1.0.6
+HOME_URL = http://omabrowser.org/standalone
+DESCRIPTION = Large-scale orthology inference
+define BLURB
+OMA is a program for inferring orthologs between genomes.
+endef
+LICENSE = MPL2
+CITE = doi:10.1186/1471-2105-9-518
+
+
+######################################################################
+
+MASTER_SITES = $(HOME_URL)/
+MASTER_SUBDIR =
+DISTNAME = $(NAME).$(GARVERSION)
+DISTFILES = $(DISTNAME).tgz
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+ifeq ($(GARARCH),x86_64)
+ DARWIN_BINARY = omadarwin.linux64
+else
+ DARWIN_BINARY = omadarwin.linu32
+endif
+
+pre-install:
+ sed -i 's|OMA_PATH=$$(dirname
$$0)/\.\.|OMA_PATH="$(prefix)/share/oma"|' $(WORKSRC)/bin/oma
+ sed -i 's|\$$OMA_PATH/bin/omadarwin|$(prefix)/bin/omadarwin|'
$(WORKSRC)/bin/oma
+ sed -i 's|DARWIN_PATH=$$(dirname
$$0)|DARWIN_PATH="$(prefix)/share/oma"|' $(WORKSRC)/bin/omadarwin
+ sed -i
's|DARWIN_LIB="$$DARWIN_PATH/\.\./darwinlib"|DARWIN_LIB="$(prefix)/share/oma/darwinlib"|'
$(WORKSRC)/bin/omadarwin
+ sed -i
's|DARWIN_BINARY="$$DARWIN_PATH/|DARWIN_BINARY="$(prefix)/bin/|g'
$(WORKSRC)/bin/omadarwin
+ $(MAKECOOKIE)
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/bin/omadarwin
+ $(INSTALL_BIN) $(WORKSRC)/bin/$(DARWIN_BINARY)
+ $(INSTALL_BIN) $(WORKSRC)/bin/oma
+ install -d $(packageprefix)/share/oma
+ install -m644 $(WORKSRC)/OMA.drw $(packageprefix)/share/oma/OMA.drw
+ install -m644 $(WORKSRC)/README.oma
$(packageprefix)/share/oma/README.oma
+ install -m644 $(WORKSRC)/parameters.drw
$(packageprefix)/share/oma/parameters.drw
+ install -d $(packageprefix)/share/oma/lib
+ for f in $(WORKSRC)/lib/*; do \
+ install -m644 $$f $(packageprefix)/share/oma/lib/`basename
$$f`; \
+ done
+ install -d $(packageprefix)/share/oma/darwinlib
+ install -d $(packageprefix)/share/oma/darwinlib/Optimizations
+ install -d $(packageprefix)/share/oma/darwinlib/Server
+ install -d $(packageprefix)/share/oma/darwinlib/CodonData
+ install -d $(packageprefix)/share/oma/darwinlib/mats
+ install -d $(packageprefix)/share/oma/darwinlib/Wrappers
+ for f in $(WORKSRC)/darwinlib/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/`basename $$f`; \
+ done
+ for f in $(WORKSRC)/darwinlib/Optimizations/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/Optimizations/`basename $$f`; \
+ done
+ for f in $(WORKSRC)/darwinlib/Server/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/Server/`basename $$f`; \
+ done
+ for f in $(WORKSRC)/darwinlib/CodonData/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/CodonData/`basename $$f`; \
+ done
+ for f in $(WORKSRC)/darwinlib/mats/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/mats/`basename $$f`; \
+ done
+ for f in $(WORKSRC)/darwinlib/Wrappers/*; do \
+ install -m644 $$f
$(packageprefix)/share/oma/darwinlib/Wrappers/`basename $$f`; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/oma/sha256sums'
--- a/pkg/bio/oma/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/oma/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+c84bace8dd3aafdb38a106d24843a2dd6f3172593896e80f0b6ab24837f53055
download/OMA.1.0.6.tgz
=== added directory 'pkg/bio/openms'
=== added file 'pkg/bio/openms/Makefile'
--- a/pkg/bio/openms/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/openms/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,51 @@
+# Copyright © 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = OpenMS
+GARNAME = openms
+UPSTREAMNAME = OpenMS
+GARVERSION = 1.11.1
+HOME_URL = http://open-ms.sourceforge.net
+DESCRIPTION = A C++ library and tools for LC/MS data analysis
+define BLURB
+OpenMS is a C++ library for LC/MS data management and analyses. It
+offers an infrastructure for the rapid development of mass
+spectrometry related software.
+endef
+LICENSE = 3-clause BSD
+CITE = doi:10.1186/1471-2105-9-163
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = open-ms/files/$(UPSTREAMNAME)/$(DISTNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = seqan glpk gsl xerces libsvm
+
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
+
+CMAKE_CONFIGURE_ARGS += -DCMAKE_FIND_ROOT_PATH=$(prefix) \
+ -DBOOST_USE_STATIC=OFF -DINSTALL_PREFIX=$(prefix)
+
+LDFLAGS += -lQtCore -lQtGui
+
+MAKE_ARGS = OpenMS TOPP UTILS GUI
=== added file 'pkg/bio/openms/sha256sums'
--- a/pkg/bio/openms/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/openms/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+e2403df3e3e902dd92480b4137753da7af66f12c422b795d0daa93fd9b2cc185
download/OpenMS-1.11.1.tar.gz
=== added directory 'pkg/bio/pagan-msa'
=== added file 'pkg/bio/pagan-msa/Makefile'
--- a/pkg/bio/pagan-msa/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pagan-msa/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,60 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PAGAN
+GARNAME = pagan-msa
+GARVERSION = 20121025
+HOME_URL = https://code.google.com/p/pagan-msa/
+DESCRIPTION = A general-purpose method for the alignment of sequence graphs
+define BLURB
+PAGAN is a general-purpose method for the alignment of sequence
+graphs. It can be used for, for example, phylogenetic multiple
+sequence alignment, alignment extension by phylogenetic sequence
+placement or inference of ancestral sequences.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1093/bioinformatics/bts198
+
+######################################################################
+
+MASTER_SITES = http://$(GARNAME).googlecode.com/
+MASTER_SUBDIR = files/
+DISTFILES = pagan.src.$(GARVERSION).tgz
+PATCHFILES = $(DISTNAME)-include-unistd_h.patch
+WORKSRC = $(WORKDIR)/$(GARNAME)/src
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS = #boost
+
+PATCHOPTS = -p3
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+pre-build:
+ mv $(WORKSRC)/Makefile.no_Qt $(WORKSRC)/Makefile
+ sed -i '19s|\(.*\)|\1 -lboost_system|' $(WORKSRC)/Makefile
+ $(MAKECOOKIE)
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/pagan
+ $(MAKECOOKIE)
=== added directory 'pkg/bio/pagan-msa/files'
=== added file
'pkg/bio/pagan-msa/files/pagan-msa-20121025-include-unistd_h.patch'
--- a/pkg/bio/pagan-msa/files/pagan-msa-20121025-include-unistd_h.patch
1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pagan-msa/files/pagan-msa-20121025-include-unistd_h.patch
2016-06-17 19:57:40 +0000
@@ -0,0 +1,11 @@
+diff -x config.log -x config.status -ru
work/pagan-msa/src/utils/check_version.cpp
work/pagan-msa/src/utils/check_version.cpp
+--- work/pagan-msa/src/utils/check_version.cpp 2012-10-26 09:56:43.000000000
+0100
++++ work/pagan-msa/src/utils/check_version.cpp 2014-02-24 22:39:31.984417220
+0000
+@@ -21,6 +21,7 @@
+ #include "utils/check_version.h"
+ #include "utils/log_output.h"
+
++#include <unistd.h>
+ #include <stdio.h>
+ #include <sys/socket.h>
+ #include <arpa/inet.h>
=== added file 'pkg/bio/pagan-msa/sha256sums'
--- a/pkg/bio/pagan-msa/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pagan-msa/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,2 @@
+5443c2ad832ab5dbd54a15aee2660ace8a24632d16b21b12ca2917c6503feec4
download/pagan.src.20121025.tgz
+93a9b0895d11271d71afdbf82bf09c123134c7d914147f38e4af317bb778dcfa
download/pagan-msa-20121025-include-unistd_h.patch
=== added directory 'pkg/bio/pfamscan'
=== added file 'pkg/bio/pfamscan/Makefile'
--- a/pkg/bio/pfamscan/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pfamscan/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,60 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PfamScan
+GARNAME = pfamscan
+GARVERSION = 2013-10-15
+HOME_URL = http://pfam.sanger.ac.uk
+DESCRIPTION = Search Pfam locally
+define BLURB
+PfamScan is a perl script for searching the Pfam libraries locally.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1093/nar/gkr1065
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.sanger.ac.uk/pub/databases/Pfam/
+MASTER_SUBDIR = Tools/
+DISTFILES = $(NAME).tar.gz
+WORKSRC = $(WORKDIR)/PfamScan
+INSTALL_SCRIPTS = script
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-script:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ install -d $(packageprefix)/lib/perl5
+ install -m755 $(WORKSRC)/pfam_scan.pl
$(packageprefix)/lib/perl5/pfam_scan.pl
+ install -d $(packageprefix)/bin
+ ln -s $(packagedir)/lib/perl5/pfam_scan.pl
$(packageprefix)/bin/pfam_scan.pl
+ install -d $(packageprefix)/lib/perl5/Bio/Pfam/Active_site
+ install -m644 $(WORKSRC)/Bio/Pfam/Active_site/as_search.pm
$(packageprefix)/lib/perl5/Bio/Pfam/Active_site/as_search.pm
+ install -d $(packageprefix)/lib/perl5/Bio/Pfam/HMM
+ for f in $(WORKSRC)/Bio/Pfam/HMM/*; do \
+ install -m644 $$f
$(packageprefix)/lib/perl5/Bio/Pfam/HMM/`basename $$f`; \
+ done
+ install -d $(packageprefix)/lib/perl5/Bio/Pfam/Scan
+ install -m644 $(WORKSRC)/Bio/Pfam/Scan/PfamScan.pm
$(packageprefix)/lib/perl5/Bio/Pfam/Scan/PfamScan.pm
+ install -m644 $(WORKSRC)/Bio/Pfam/Scan/Seq.pm
$(packageprefix)/lib/perl5/Bio/Pfam/Scan/Seq.pm
+ $(MAKECOOKIE)
=== added file 'pkg/bio/pfamscan/PfamScan.tar.gz'
Binary files a/pkg/bio/pfamscan/PfamScan.tar.gz 1970-01-01 00:00:00 +0000 and
b/pkg/bio/pfamscan/PfamScan.tar.gz 2016-06-17 19:57:40 +0000 differ
=== added file 'pkg/bio/pfamscan/sha256sums'
--- a/pkg/bio/pfamscan/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pfamscan/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+9d63fbc90e835000246da21d79b4de19b29559f3b4b107e7c13fde64ec858580
download/PfamScan.tar.gz
=== added directory 'pkg/bio/phyml'
=== added file 'pkg/bio/phyml/Makefile'
--- a/pkg/bio/phyml/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/phyml/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,45 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PhyML
+GARNAME = phyml
+GARVERSION = 20140223
+HOME_URL = https://code.google.com/p/phyml/
+DESCRIPTION = Estimate phylogenies by maximum likelihood
+define BLURB
+PhyML is a program for estimating maximum likelihood phylogenies from
+nucleotide or amino acid sequence alignments. It features a large
+variety of substitution models and many options for exploring the
+phylogenetic tree topologies.
+endef
+LICENSE = GPLv2
+CITE = doi:10.1007/978-1-59745-251-9_6
+
+######################################################################
+
+MASTER_SITES = https://googledrive.com/
+MASTER_SUBDIR = host/0Bwr9KQU1ZdE-Nk5rSHlsbTlhRWM/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
=== added file 'pkg/bio/phyml/sha256sums'
--- a/pkg/bio/phyml/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/phyml/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+8e435cc4ffdb97ca7f379a3d037fbb043e18550c1d8f6bb80ea02ef0a6d340ec
download/phyml-20140223.tar.gz
=== added directory 'pkg/bio/prank-msa'
=== added file 'pkg/bio/prank-msa/Makefile'
--- a/pkg/bio/prank-msa/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prank-msa/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PRANK
+GARNAME = prank-msa
+GARVERSION = 140110
+HOME_URL = https://code.google.com/p/prank-msa/
+DESCRIPTION = A probabilistic multiple alignment program
+define BLURB
+PRANK is a probabilistic multiple alignment program that can work with
+DNA, codon or amino-acid sequences. Unlike many alignment programs,
+it handles insertions correctly and it avoids over-estimation of the
+number of deletion events. It also supports including potential
+structural information to which sequences can be aligned, assisting in
+the prediction of locations of structural features in the sequences.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1007/978-1-62703-646-7_10
+
+######################################################################
+
+MASTER_SITES = http://$(GARNAME).googlecode.com/
+MASTER_SUBDIR = files/
+DISTFILES = prank.source.$(GARVERSION).tgz
+WORKSRC = $(WORKDIR)/$(GARNAME)/src
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/prank
+ $(MAKECOOKIE)
=== added file 'pkg/bio/prank-msa/sha256sums'
--- a/pkg/bio/prank-msa/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prank-msa/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+040fe80e0a64abd45db34dc974dddde3a64f8b1d9695452700b12b92dd987fe2
download/prank.source.140110.tgz
=== added directory 'pkg/bio/primer3'
=== added file 'pkg/bio/primer3/Makefile'
--- a/pkg/bio/primer3/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/primer3/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,54 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Primer3
+GARNAME = primer3
+GARVERSION = 2.3.6
+HOME_URL = http://primer3.sourceforge.net/
+DESCRIPTION = Design PCR primers
+define BLURB
+Primer3 is a program for designing PCR primers for a given sequence.
+It can also design hybridization probes and sequencing primers.
+endef
+LICENSE = GPLv2+
+CITE = doi:10.1093/nar/gks596
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(GARNAME)-src-$(GARVERSION).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/src/Makefile
+TEST_SCRIPTS = $(WORKSRC)/src/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BINS = oligotm ntthal primer3_core ntdpal long_seq_tm_test
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for bin in $(BINS); do \
+ $(INSTALL_BIN) $(WORKSRC)/src/$$bin; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/primer3/sha256sums'
--- a/pkg/bio/primer3/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/primer3/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4
download/primer3-src-2.3.6.tar.gz
=== added directory 'pkg/bio/prodigal'
=== added file 'pkg/bio/prodigal/Makefile'
--- a/pkg/bio/prodigal/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prodigal/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,48 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Prodigal
+GARNAME = prodigal
+UPSTREAMNAME = Prodigal
+GARVERSION = 2.6.1
+HOME_URL = http://prodigal.ornl.gov/
+DESCRIPTION = Fast, reliable protein-coding gene prediction for prokaryotic
genomes
+define BLURB
+Prodigal is a program for predicting genes in prokaryotic genomes.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1186/1471-2105-11-119
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = hyattpd//$(UPSTREAMNAME)/archive/
+DISTFILES = v$(GARVERSION).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bin:
+ $(INSTALL_BIN) $(WORKSRC)/$(GARNAME)
+ $(MAKECOOKIE)
=== added file 'pkg/bio/prodigal/sha256sums'
--- a/pkg/bio/prodigal/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prodigal/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+922a8749bda9fa150b5cf409c3c7321a032f38e4663606eb877b661a0baae22b
download/v2.6.1.tar.gz
=== added directory 'pkg/bio/prokka'
=== added file 'pkg/bio/prokka/Makefile'
--- a/pkg/bio/prokka/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prokka/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,69 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Prokka
+GARNAME = prokka
+GARVERSION = 1.10
+HOME_URL = http://www.bioinformatics.net.au/software.prokka.shtml
+DESCRIPTION = Rapid prokaryotic genome annotation
+define BLURB
+Prokka is a tool for the rapid annotation of prokaryotic genomes.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1093/bioinformatics/btu153
+
+######################################################################
+
+MASTER_SITES = http://www.vicbioinformatics.com/
+MASTER_SUBDIR =
+DISTFILES = $(DISTNAME).tar.gz
+INSTALL_SCRIPTS = scripts db
+
+BUILDDEPS =
+LIBDEPS = perl-bioperl ncbi-blast hmmer aragorn prodigal ncbi-tools \
+ parallel infernal barrnap minced
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+SCRIPTS = prokka prokka-biocyc_to_fasta_db prokka-build_kingdom_dbs \
+prokka-cdd_to_hmm prokka-clusters_to_hmm prokka-genbank_to_fasta_db \
+prokka-genpept_to_fasta_db prokka-hamap_to_hmm prokka-make_tarball \
+prokka-tigrfams_to_hmm prokka-uniprot_to_fasta_db
+
+pre-install:
+ sed -i '42s|\$$FindBin::RealBin/../binaries/\$$OPSYS|$(prefix)/bin|'
$(WORKSRC)/bin/prokka
+ sed -i '47s|\$$FindBin::RealBin/../db|$(prefix)/share/$(GARNAME)/db|'
$(WORKSRC)/bin/prokka
+ $(MAKECOOKIE)
+
+install-db:
+ install -d $(packageprefix)/share/$(GARNAME)/db/cm
+ install -m644 $(WORKSRC)/db/cm/Bacteria
$(packageprefix)/share/$(GARNAME)/db/cm/Bacteria
+ install -m644 $(WORKSRC)/db/cm/Viruses
$(packageprefix)/share/$(GARNAME)/db/cm/Viruses
+ for k in Archaea Bacteria Mitochondria Viruses; do \
+ install -d $(packageprefix)/share/$(GARNAME)/db/kingdom/$$k; \
+ install -m644 $(WORKSRC)/db/kingdom/$$k/sprot
$(packageprefix)/share/$(GARNAME)/db/kingdom/$$k/sprot; \
+ done
+ $(MAKECOOKIE)
+
+install-scripts:
+ for s in $(SCRIPTS); do \
+ $(INSTALL_BIN) $(WORKSRC)/bin/$$s; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/prokka/sha256sums'
--- a/pkg/bio/prokka/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/prokka/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+7f95adff99c05a359904483ac52ba011b606c5314eccfb2f29ab31ff957f6b00
download/prokka-1.10.tar.gz
=== added directory 'pkg/bio/provean'
=== added file 'pkg/bio/provean/Makefile'
--- a/pkg/bio/provean/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/provean/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,43 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = PROVEAN
+GARNAME = provean
+GARVERSION = 1.1.5
+HOME_URL = http://provean.jcvi.org/index.php
+DESCRIPTION = Protein variation effect analyzer
+define BLURB
+PROVEAN (Protein Variation Effect Analyzer) is a tool for predicting
+the effects of amino an acid substitution or indel on the biological
+function of a protein.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1371/journal.pone.0046688
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = ncbi-blast cd-hit
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/provean/sha256sums'
--- a/pkg/bio/provean/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/provean/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+f543a4446f239bbe57ab16bb0ea2be5f6aeebddb58f8025dc38781ad4c8e007c
download/provean-1.1.5.tar.gz
=== added directory 'pkg/bio/pscan'
=== added file 'pkg/bio/pscan/Makefile'
--- a/pkg/bio/pscan/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pscan/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,53 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Pscan
+GARNAME = pscan
+GARVERSION = 1.3
+HOME_URL = http://159.149.160.51/pscan/
+DESCRIPTION = Motif discovery in sequences
+define BLURB
+Pscan is a tool for finding transcription factor binding motifs in
+sequences from co-regulated genes.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1093/nar/gkp464
+
+######################################################################
+
+MASTER_SITES = http://159.149.160.51/
+MASTER_SUBDIR = $(GARNAME)/Source/
+DISTNAME = $(GARNAME)
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = bin
+INSTALL_SCRIPTS = bin
+
+BUILDDEPS =
+LIBDEPS = gsl
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+build-bin:
+ $(CXX) $(WORKSRC)/pscan.cpp -o $(WORKSRC)/pscan -O3 -lgsl -lgslcblas
+ $(MAKECOOKIE)
+
+install-bin:
+ $(INSTALL_BIN) $(WORKSRC)/pscan
+ $(MAKECOOKIE)
=== added file 'pkg/bio/pscan/sha256sums'
--- a/pkg/bio/pscan/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/pscan/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+53bf86aa20bdb393e9b2831b8a34cb74835ff8c7601d7caa3ba7c61790514ea9
download/pscan.tar.gz
=== added directory 'pkg/bio/qmmraxml'
=== added file 'pkg/bio/qmmraxml/Makefile'
--- a/pkg/bio/qmmraxml/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/qmmraxml/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,52 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = QmmRAxML
+GARNAME = qmmraxml
+GARVERSION = 2.0
+HOME_URL = http://www.mathstat.dal.ca/~hcwang/QmmRAxML/
+DESCRIPTION = Q-matrix mixture RAxML
+define BLURB
+QmmRAxML is a variant of RAxML that accounts for site-specific amino
+acid frequencies in phylogenetic inference via a class-frequency
+mixture model.
+endef
+LICENSE = GPLv2 or later
+CITE = doi:10.1186/1471-2148-8-331
+
+######################################################################
+
+MASTER_SITES = http://www.mathstat.dal.ca/
+MASTER_SUBDIR = ~hcwang/QmmRAxML/src/
+DISTNAME = $(GARNAME)$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+EXTRACTDIR = $(WORKSRC)
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/qmmraxmlHPC
+ $(MAKECOOKIE)
=== added file 'pkg/bio/qmmraxml/sha256sums'
--- a/pkg/bio/qmmraxml/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/qmmraxml/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+20256c8498fffd042acbc6467a0f5d9fdb14d933908c66141132c067ba340c98
download/qmmraxml2.0.tar.gz
=== added directory 'pkg/bio/quake'
=== added file 'pkg/bio/quake/Makefile'
--- a/pkg/bio/quake/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/quake/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,57 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Quake
+GARNAME = quake
+GARVERSION = 0.3.5
+HOME_URL = http://www.cbcb.umd.edu/software/quake/
+DESCRIPTION = Correct Illumina substitution sequencing errors
+define BLURB
+Quake is a package for correcting substitution sequencing errors in
+experiments with deep coverage, particularly for Illumina sequencing
+reads. It utilizes a robust mixture model of erroneous and genuine
+k-mer distributions to determine where errors are located.
+endef
+LICENSE = Artistic License 2.0
+CITE = doi:10.1186/gb-2010-11-11-r116
+
+######################################################################
+
+MASTER_SITES = http://www.cbcb.umd.edu/
+MASTER_SUBDIR = software/$(GARNAME)/downloads/
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(NAME)
+BUILD_SCRIPTS = $(WORKSRC)/src/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BINS = build_bithash correct correct_stats count-kmers count_qmers \
+ count-qmers reduce-kmers reduce-qmers trim
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for bin in $(BINS); do \
+ $(INSTALL_BIN) $(WORKSRC)/src/$$bin; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/quake/sha256sums'
--- a/pkg/bio/quake/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/quake/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+8ded707213117463675553bb989c4c69c5d01b122945b1e265c79d7e4e34eebd
download/quake-0.3.5.tar.gz
=== added directory 'pkg/bio/raxml'
=== added file 'pkg/bio/raxml/Makefile'
--- a/pkg/bio/raxml/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/raxml/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,87 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = RAxML
+GARNAME = raxml
+UPSTREAMNAME = standard-RAxML
+GARVERSION = 8.1.9
+HOME_URL = http://www.exelixis-lab.org/
+DESCRIPTION = Sequential and parallel Maximum Likelihood inference of
phylogenetic trees
+define BLURB
+RAxML (Randomized Axelerated Maximum Likelihood) is a program for
+sequential and parallel Maximum Likelihood based inference of large
+phylogenetic trees. It can also be used for post-analyses of sets of
+phylogenetic trees, analyses of alignments and, evolutionary placement
+of short reads.
+endef
+LICENSE = GPLv3 or later
+CITE = doi:10.1093/bioinformatics/btu033
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = stamatak/standard-RAxML/archive/
+DISTFILES = v$(GARVERSION).tar.gz
+INSTALL_SCRIPTS = program
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include config.mk
+
+ifeq ($(shell cat /proc/cpuinfo | grep -q avx2 && echo avx2),avx)
+ OPTIMIZE = AVX2
+else ifeq ($(shell cat /proc/cpuinfo | grep -q avx && echo avx),avx)
+ OPTIMIZE = AVX
+else ifeq ($(shell cat /proc/cpuinfo | grep -q sse3 && echo sse3),sse3)
+ OPTIMIZE = SSE3
+else
+ OPTIMIZE =
+endif
+
+ifneq ($(OPTIMIZE),)
+ .OPTIMIZE = .$(OPTIMIZE)
+else
+ .OPTIMIZE =
+endif
+ifneq ($(MULTITHREAD),)
+ .MULTITHREAD = .$(MULTITHREAD)
+else
+ .MULTITHREAD =
+endif
+
+BUILD_SCRIPTS = $(WORKSRC)/Makefile$(.OPTIMIZE)$(.MULTITHREAD).gcc
+
+include ../../../gar/gar.mk
+
+BINARY = $(subst .,-,raxmlHPC$(.OPTIMIZE))
+
+build-$(WORKSRC)/Makefile.%:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running make $(OFF)\n"
+ $(BUILD_ENV) $(MAKE) -C $(WORKSRC) -f Makefile.$* $(MAKE_ARGS)
$(BUILD_ARGS) $(OUTPUT) || \
+ $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-program:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME) $(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/$(BINARY)
+ if [[ "$(BINARY)" != "raxmlHPC" ]]; then \
+ ln -s $(packagedir)/bin/$(BINARY)
$(packageprefix)/bin/raxmlHPC; \
+ fi
+ $(MAKECOOKIE)
=== added file 'pkg/bio/raxml/sha256sums'
--- a/pkg/bio/raxml/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/raxml/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+6fe424bbdf7e5ad94680431856d8ac20c23f540ace85cba7accaaa6cd28cdebe
download/v8.1.9.tar.gz
=== added directory 'pkg/bio/reapr'
=== added file 'pkg/bio/reapr/Makefile'
--- a/pkg/bio/reapr/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/reapr/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,64 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = REAPR
+GARNAME = reapr
+UPSTREAMNAME = Reapr
+GARVERSION = 1.0.17
+HOME_URL = https://www.sanger.ac.uk/resources/software/reapr/
+DESCRIPTION = Recognising errors in assemblies using paired reads
+define BLURB
+REAPR is a tool for evaluating the accuracy of a genome assembly via
+mapped paired end reads, without the use of a reference genome for
+comparison.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1186/gb-2013-14-5-r47
+
+######################################################################
+
+MASTER_SITES = ftp://ftp.sanger.ac.uk/
+MASTER_SUBDIR = pub/resources/software/$(GARNAME)/
+DISTNAME = $(UPSTREAMNAME)_$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+BUILD_SCRIPTS = $(WORKSRC)/src/tabix/Makefile $(WORKSRC)/src/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS = bamtools snpomatic samtools
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BUILD_ARGS += BAMTOOLS_ROOT=$(prefix)
+
+BINS = task_score task_stats task_break bam2fragCov bam2insert \
+ bam2fcdEstimate make_plots fa2gaps fa2gc scaff2contig n50 \
+ task_gapresize task_fcdrate bam2perfect reapr.pl
+
+pre-build:
+ sed -i
'/^CFLAGS/{s|/include|/include/bamtools|;s|/lib|/lib/bamtools|g}'
$(WORKSRC)/src/Makefile
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ for bin in $(BINS); do \
+ $(INSTALL_BIN) $(WORKSRC)/src/$$bin; \
+ done
+ $(SYMLINK_BIN) $(packagedir)/bin/reapr.pl reapr
+ $(MAKECOOKIE)
=== added file 'pkg/bio/reapr/sha256sums'
--- a/pkg/bio/reapr/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/reapr/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+e235d846447a34fffa6765fbbea2407cc0c6a0217c007f196e5786022034b65e
download/Reapr_1.0.17.tar.gz
=== added directory 'pkg/bio/rnaz'
=== added file 'pkg/bio/rnaz/Makefile'
--- a/pkg/bio/rnaz/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/rnaz/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = RNAz
+GARNAME = rnaz
+UPSTREAMNAME = RNAz
+GARVERSION = 2.1
+HOME_URL = http://www.tbi.univie.ac.at/~wash/RNAz/
+DESCRIPTION = Predicting structural noncoding RNAs
+define BLURB
+RNAz is a program for predicting structurally conserved and
+thermodynamically stable RNA secondary structures in multiple sequence
+alignments.
+endef
+LICENSE =
+CITE = doi:10.1142/9789814295291_0009
+
+######################################################################
+
+MASTER_SITES = http://www.tbi.univie.ac.at/
+MASTER_SUBDIR = ~wash/$(UPSTREAMNAME)/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/rnaz/sha256sums'
--- a/pkg/bio/rnaz/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/rnaz/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+b32ec0361889319f2058f224d6c456c853dbc30dff4dba90c53a8f9fd7b83be5
download/RNAz-2.1.tar.gz
=== added directory 'pkg/bio/samtools'
=== added file 'pkg/bio/samtools/Makefile'
--- a/pkg/bio/samtools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/samtools/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,60 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SAMtools
+GARNAME = samtools
+GARVERSION = 1.1
+HOME_URL = http://samtools.sourceforge.net/
+DESCRIPTION = Utilities for manipulating alignments in the SAM format
+define BLURB
+SAMtools provides utilities for manipulating alignments in the SAM
+format, which is a generic format for storing large nucleotide
+sequence alignments. The functionality of the tools includes sorting,
+merging, indexing and generating alignments in a per-position format.
+endef
+LICENSE = Expat License
+CITE = doi:10.1093/bioinformatics/btp352
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.bz2
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = $(WORKSRC)/Makefile lib headers #programs lib headers man
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+INSTALL_ARGS += prefix=$(packageprefix)
+
+install-lib:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing libbam.$(OFF)\n"
+ $(INSTALL_LIB) $(WORKSRC)/libbam.a
+ $(MAKECOOKIE)
+
+install-headers:
+ install -d $(packageprefix)/include/bam
+ for f in $(WORKSRC)/*.h; do \
+ install -m644 $$f $(packageprefix)/include/bam/`basename $$f`; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/samtools/sha256sums'
--- a/pkg/bio/samtools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/samtools/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8
download/samtools-1.1.tar.bz2
=== added directory 'pkg/bio/seq_crumbs'
=== added file 'pkg/bio/seq_crumbs/Makefile'
--- a/pkg/bio/seq_crumbs/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seq_crumbs/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,47 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Seq Crumbs
+GARNAME = seq_crumbs
+UPSTREAMNAME = seq_crumbs
+GARVERSION = 0.1.9
+HOME_URL = http://bioinf.comav.upv.es/seq_crumbs/
+DESCRIPTION = A set of small sequence processing utilities.
+define BLURB
+Seq_crumbs is modeled after the Unix command line text processing
+utilities so every utility tries to perform a specific task and most
+of them take a sequence file as input and create a new processed
+sequence file as output. This design encourages the assembly of the
+seq_crumbs utilities with Unix pipes to create complex pipelines.
+endef
+LICENSE = GPLv3 or later
+
+######################################################################
+
+MASTER_SITES = http://bioinf.comav.upv.es/
+MASTER_SUBDIR = downloads/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2-biopython python2-pysam python2-toolz
+
+PYTHON ?= $(prefix)/bin/python2
+
+######################################################################
+
+include ../../../gar/gar.lib/python.mk
+include config.mk
=== added file 'pkg/bio/seq_crumbs/sha256sums'
--- a/pkg/bio/seq_crumbs/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seq_crumbs/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+484b3206e59fb85bab17413b69a39f593e934d83427a7d0ffdf09cc19767e532
download/seq_crumbs-0.1.9.tar.gz
=== added directory 'pkg/bio/seqsuite'
=== added file 'pkg/bio/seqsuite/Makefile'
--- a/pkg/bio/seqsuite/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seqsuite/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,84 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SeqSuite
+GARNAME = seqsuite
+GARVERSION = 2013-12-03
+HOME_URL = https://sites.google.com/site/seqsuite/
+DESCRIPTION = A suite of sequence analysis programs
+define BLURB
+SeqSuite is a suite of sequence analysis programs. It includes
+SLiMSuite, which contains software for short linear motif analysis.
+endef
+LICENSE = GPLv2 or later
+CITE =
+
+######################################################################
+
+MASTER_SITES = http://www.southampton.ac.uk/
+MASTER_SUBDIR = ~re1u06/software/packages/
+DISTNAME = $(GARNAME).$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(GARNAME)
+INSTALL_SCRIPTS = scripts
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+LIBDIR = lib/python2.7/site-packages/seqsuite
+
+pre-install:
+ for f in $(WORKSRC)/extras/*.py $(WORKSRC)/tools/*.py; do \
+ sed -i '1s|#!.*|#!/usr/bin/env python2|' $$f; \
+ done
+ sed -i 's|blastpath=.*|blastpath=$(prefix)/bin|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|clustalw=.*|clustalw=$(prefix)/bin/clustalw|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|iupath=.*|iupath=$(prefix)/bin/iupred|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|pypath=.*|pypath=$(prefix)/$(LIBDIR)/|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|fsa=.*|fsa=$(prefix)/bin/fsa|' $(WORKSRC)/settings/rje.ini
+ sed -i 's|mafft=.*|mafft=$(prefix)/bin/mafft|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|fasttree=.*|fasttree=$(prefix)/bin/FastTree|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|phylip=.*|phylip=$(prefix)/bin/|' $(WORKSRC)/settings/rje.ini
+ sed -i 's|clustalo=.*|clustalo=$(prefix)/bin/clustalo|'
$(WORKSRC)/settings/rje.ini
+ sed -i 's|pagan=.*|pagan=$(prefix)/bin/pagan|'
$(WORKSRC)/settings/rje.ini
+ $(MAKECOOKIE)
+
+install-scripts:
+ install -d $(packageprefix)/$(LIBDIR)
+ install -d $(packageprefix)/$(LIBDIR)/extras
+ install -d $(packageprefix)/$(LIBDIR)/libraries
+ install -d $(packageprefix)/$(LIBDIR)/settings
+ install -d $(packageprefix)/$(LIBDIR)/tools
+ install -d $(packageprefix)/bin
+ for f in $(WORKSRC)/extras/*; do \
+ install -m755 $$f $(packageprefix)/$(LIBDIR)/extras/`basename
$$f`; \
+ ln -s $(packagedir)/$(LIBDIR)/extras/`basename $$f`
$(packageprefix)/bin/`basename $$f .py`; \
+ done
+ for f in $(WORKSRC)/tools/*; do \
+ install -m755 $$f $(packageprefix)/$(LIBDIR)/tools/`basename
$$f`; \
+ ln -s $(packagedir)/$(LIBDIR)/tools/`basename $$f`
$(packageprefix)/bin/`basename $$f .py`; \
+ done
+ for f in $(WORKSRC)/libraries/*; do \
+ install -m644 $$f
$(packageprefix)/$(LIBDIR)/libraries/`basename $$f`; \
+ done
+ install -m644 $(WORKSRC)/settings/rje.ini
$(packageprefix)/$(LIBDIR)/settings/rje.ini
+ $(MAKECOOKIE)
=== added file 'pkg/bio/seqsuite/sha256sums'
--- a/pkg/bio/seqsuite/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seqsuite/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+b1edb2763a6f691d0482376c4082f742f99711342020da57b14adc3392718671
download/seqsuite.2013-12-03.tar.gz
=== added directory 'pkg/bio/seqtk'
=== added file 'pkg/bio/seqtk/Makefile'
--- a/pkg/bio/seqtk/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seqtk/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,52 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Seqtk
+GARNAME = seqtk
+GARVERSION = 1.0
+gitcommit = 2f0d11c
+HOME_URL = https://github.com/lh3/seqtk
+DESCRIPTION = A toolkit for processing sequences in FASTA/Q formats
+define BLURB
+Seqtk is a tool for processing sequences in FASTA or FASTQ format. It can
+perform basic file format conversions, file clean-up such as line-wrapping,
+and data extraction or manipulation.
+endef
+LICENSE = Expat License
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = lh3/$(GARNAME)/tarball/$(GARVERSION)/
+DISTFILES = $(GARVERSION).tar.gz
+DISTNAME = lh3-$(GARNAME)-$(gitcommit)
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bin:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/seqtk
+ $(MAKECOOKIE)
=== added file 'pkg/bio/seqtk/sha256sums'
--- a/pkg/bio/seqtk/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/seqtk/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+c0b490c4cd282ed4583c13b3b3c587fbfde9e62b98a91d5c082348a90ff6f0d1
download/1.0.tar.gz
=== added directory 'pkg/bio/slimsuite'
=== added file 'pkg/bio/slimsuite/Makefile'
--- a/pkg/bio/slimsuite/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/slimsuite/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,83 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SLiMSuite
+GARNAME = slimsuite
+GARVERSION = 2014-08-25
+HOME_URL = https://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/
+DESCRIPTION = Programs for the prediction of short linear motifs
+define BLURB
+SLiMSuite contains software for short linear motif analysis.
+endef
+LICENSE = GPLv2 or later
+CITE =
+
+######################################################################
+
+MASTER_SITES = http://www.southampton.ac.uk/
+MASTER_SUBDIR = ~re1u06/software/packages/
+DISTNAME = $(GARNAME).$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(GARNAME)
+INSTALL_SCRIPTS = scripts
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+LIBDIR = lib/python2.7/site-packages/seqsuite
+
+pre-install:
+ for f in $(WORKSRC)/extras/*.py $(WORKSRC)/tools/*.py; do \
+ sed -i '1s|#!.*|#!/usr/bin/env python2|' $$f; \
+ done
+ sed -i 's|blastpath=.*|blastpath=$(prefix)/bin|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|clustalw=.*|clustalw=$(prefix)/bin/clustalw|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|iupath=.*|iupath=$(prefix)/bin/iupred|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|pypath=.*|pypath=$(prefix)/$(LIBDIR)/|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|fsa=.*|fsa=$(prefix)/bin/fsa|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|mafft=.*|mafft=$(prefix)/bin/mafft|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|fasttree=.*|fasttree=$(prefix)/bin/FastTree|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|phylip=.*|phylip=$(prefix)/bin/|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|clustalo=.*|clustalo=$(prefix)/bin/clustalo|'
$(WORKSRC)/settings/defaults.ini
+ sed -i 's|pagan=.*|pagan=$(prefix)/bin/pagan|'
$(WORKSRC)/settings/defaults.ini
+ $(MAKECOOKIE)
+
+install-scripts:
+ install -d $(packageprefix)/$(LIBDIR)
+ install -d $(packageprefix)/$(LIBDIR)/extras
+ install -d $(packageprefix)/$(LIBDIR)/libraries
+ install -d $(packageprefix)/$(LIBDIR)/settings
+ install -d $(packageprefix)/$(LIBDIR)/tools
+ install -d $(packageprefix)/bin
+ for f in $(WORKSRC)/extras/*; do \
+ install -m755 $$f $(packageprefix)/$(LIBDIR)/extras/`basename
$$f`; \
+ ln -s $(packagedir)/$(LIBDIR)/extras/`basename $$f`
$(packageprefix)/bin/`basename $$f .py`; \
+ done
+ for f in $(WORKSRC)/tools/*; do \
+ install -m755 $$f $(packageprefix)/$(LIBDIR)/tools/`basename
$$f`; \
+ ln -s $(packagedir)/$(LIBDIR)/tools/`basename $$f`
$(packageprefix)/bin/`basename $$f .py`; \
+ done
+ for f in $(WORKSRC)/libraries/*; do \
+ install -m644 $$f
$(packageprefix)/$(LIBDIR)/libraries/`basename $$f`; \
+ done
+ install -m644 $(WORKSRC)/settings/defaults.ini
$(packageprefix)/$(LIBDIR)/settings/defaults.ini
+ $(MAKECOOKIE)
=== added file 'pkg/bio/slimsuite/sha256sums'
--- a/pkg/bio/slimsuite/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/slimsuite/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+eb972f3d3cb0bd9ab5399212bca17c63b401fdc886180afa1271ba1fe4a4ca83
download/slimsuite.2014-08-25.tar.gz
=== added directory 'pkg/bio/smalt'
=== added file 'pkg/bio/smalt/Makefile'
--- a/pkg/bio/smalt/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/smalt/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,44 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SMALT
+GARNAME = smalt
+GARVERSION = 0.7.6
+HOME_URL = https://www.sanger.ac.uk/resources/software/smalt/
+DESCRIPTION = A mapper for DNA sequencing reads
+define BLURB
+SMALT employs a hash index of short nucleotide words sampled along a
+reference genome to identify potentially matching segments from DNA
+sequencing reads. The reads are then aligned using a banded Smith-
+Waterman algorithm.
+endef
+LICENSE = GPLv3+
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = $(GARNAME)/files/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = bambamc
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
=== added file 'pkg/bio/smalt/sha256sums'
--- a/pkg/bio/smalt/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/smalt/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31
download/smalt-0.7.6.tar.gz
=== added directory 'pkg/bio/snpomatic'
=== added file 'pkg/bio/snpomatic/Makefile'
--- a/pkg/bio/snpomatic/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/snpomatic/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,53 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = SNP-o-matic
+GARNAME = snpomatic
+GARVERSION = r14
+SVN_REVISION = 14
+HOME_URL = http://snpomatic.sourceforge.net/
+DESCRIPTION = A fast, stringent short-read mapping software
+define BLURB
+SNP-o-matic is a fast, stringent tool for mapping short-read sequences
+and offers a variety of analytical output functions, with an emphasis
+on genotyping.
+endef
+LICENSE = GPLv3
+CITE =
+
+######################################################################
+
+MASTER_SITES = svnco://svn.code.sf.net/
+MASTER_SUBDIR = p/$(GARNAME)/code/
+SVN_PATH = $(subst svnco,http,$(MASTER_SITES))$(MASTER_SUBDIR)
+DISTFILES = $(DISTNAME).tar.gz
+NOCHECKSUM = $(DISTFILES)
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bin:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/findknownsnps
+ $(MAKECOOKIE)
=== added directory 'pkg/bio/t-coffee'
=== added file 'pkg/bio/t-coffee/Makefile'
--- a/pkg/bio/t-coffee/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/t-coffee/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,64 @@
+# Copyright © 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of BioSRC.
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = T-Coffee
+GARNAME = t-coffee
+UPSTREAMNAME = T-COFFEE
+GARVERSION = 10.00.r1613
+HOME_URL = http://www.tcoffee.org/
+DESCRIPTION = A multiple sequence alignment package
+define BLURB
+T-Coffee is a multiple sequence alignment package. Besides performing
+alignments, it can also combine the output of many alignmnent methods
+into one unique alignment. It can also combine sequence information
+with protein structural information, profile information or RNA
+secondary structures.
+endef
+LICENSE = GPLv2 or later
+CITE = pmid:10964570
+
+######################################################################
+
+MASTER_SITES = http://www.tcoffee.org/Packages/
+MASTER_SUBDIR = Stable/Latest/
+DISTNAME = $(UPSTREAMNAME)_distribution_Version_$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(DISTNAME)/t_coffee_source
+BUILD_SCRIPTS = $(WORKSRC)/makefile
+INSTALL_SCRIPTS = programs
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BUILD_ARGS += FCC=gfortran
+
+build-$(WORKSRC)/makefile:
+ @printf "[$(OK)build$(OFF)] $(MSG)Running make in $(OFF)$*\n"
+ $(BUILD_ENV) $(MAKE) -C $(WORKSRC) $(MAKE_ARGS) $(BUILD_ARGS) all
$(OUTPUT) || \
+ $(BUILD_FAIL)
+ $(MAKECOOKIE)
+
+install-programs:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME) programs.
$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/t_coffee
+ $(INSTALL_BIN) $(WORKSRC)/TMalign
+ $(MAKECOOKIE)
=== added file 'pkg/bio/t-coffee/sha256sums'
--- a/pkg/bio/t-coffee/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/t-coffee/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+53bf0e606737d2ba0f3909c48b1fca2421d9f756f33ccd3369be81535f395cee
download/T-COFFEE_distribution_Version_10.00.r1613.tar.gz
=== added directory 'pkg/bio/tabix'
=== added file 'pkg/bio/tabix/Makefile'
--- a/pkg/bio/tabix/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/tabix/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,62 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Tabix
+GARNAME = tabix
+GARVERSION = 0.2.6
+HOME_URL = http://samtools.sourceforge.net/tabix.shtml
+DESCRIPTION = Generic indexer for TAB-delimited genome position files
+define BLURB
+Tabix indexes a TAB-delimited genome position file and creates an
+index file.
+endef
+LICENSE = Expat
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = samtools/files/$(GARNAME)/
+DISTFILES = $(DISTNAME).tar.bz2
+CONFIGURE_SCRIPTS = $(WORKSRC)/perl/Makefile.PL \
+ $(WORKSRC)/python/setup.py
+BUILD_SCRIPTS = $(WORKSRC)/Makefile $(WORKSRC)/perl/Makefile \
+ $(WORKSRC)/python/setup.py
+INSTALL_SCRIPTS = bins lib mans $(WORKSRC)/perl/Makefile \
+ $(WORKSRC)/python/setup.py
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/tabix
+ $(INSTALL_BIN) $(WORKSRC)/bgzip
+ $(MAKECOOKIE)
+
+install-lib:
+ $(INSTALL_LIB) $(WORKSRC)/libtabix.a
+ $(MAKECOOKIE)
+
+install-mans:
+ $(INSTALL_MAN) $(WORKSRC)/tabix.1
+ $(MAKECOOKIE)
=== added file 'pkg/bio/tabix/sha256sums'
--- a/pkg/bio/tabix/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/tabix/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73
download/tabix-0.2.6.tar.bz2
=== added directory 'pkg/bio/tophat'
=== added file 'pkg/bio/tophat/Makefile'
--- a/pkg/bio/tophat/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/tophat/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,52 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = TopHat
+GARNAME = tophat
+GARVERSION = 2.0.11
+HOME_URL = http://ccb.jhu.edu/software/tophat/index.shtml
+DESCRIPTION = A fast splice junction mapper for RNA-Seq reads
+define BLURB
+TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns
+RNA-Seq reads to genomes using using Bowtie and then analyzes the
+results to identify splice junctions between exons
+endef
+LICENSE = Boost Software License 1.0
+CITE = doi:10.1093/bioinformatics/btp120
+
+######################################################################
+
+MASTER_SITES = http://ccb.jhu.edu/
+MASTER_SUBDIR = software/$(GARNAME)/downloads/
+DISTFILES = $(DISTNAME).tar.gz
+
+BUILDDEPS =
+LIBDEPS = python2 seqan samtools
+
+USE_AUTORECONF = y
+
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+CONFIGURE_ARGS += PYTHON=$(prefix)/bin/python2 \
+ --with-bam=$(prefix)
+
+pre-configure:
+ sed -i 's|-I./SeqAn-1.3||' $(WORKSRC)/configure.ac
+ $(MAKECOOKIE)
=== added file 'pkg/bio/tophat/sha256sums'
--- a/pkg/bio/tophat/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/tophat/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+0498a9a7c6dd92a810e58902f422bc7d530de9014174cbb3f959ba776d5abf07
download/tophat-2.0.11.tar.gz
=== added directory 'pkg/bio/treebest'
=== added file 'pkg/bio/treebest/Makefile'
--- a/pkg/bio/treebest/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/treebest/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,51 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = TreeBeST
+GARNAME = treebest
+GARVERSION = 1.9.2
+HOME_URL = http://treesoft.sourceforge.net/treebest.shtml
+DESCRIPTION = Tree-building guided by species trees
+define BLURB
+TreeBeST is a program for building, manipulating and displaying
+phylogenetic trees.
+endef
+LICENSE = GPLv2
+CITE =
+
+######################################################################
+
+MASTER_SITES = $(MASTER_SOURCEFORGE)
+MASTER_SUBDIR = treesoft/files/$(GARNAME)/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.gz
+SIGFILES =
+BUILD_SCRIPTS = $(WORKSRC)/Makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+install-bins:
+ @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
+ $(INSTALL_BIN) $(WORKSRC)/treebest
+ $(INSTALL_BIN) $(WORKSRC)/make_ng86
+ $(MAKECOOKIE)
=== added file 'pkg/bio/treebest/sha256sums'
--- a/pkg/bio/treebest/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/treebest/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+8dfc58113d3552a32da1e9d22b5fe97436ddcc916f6ec3b5c3d043dd5767bb04
download/treebest-1.9.2.tar.gz
=== added directory 'pkg/bio/trimal'
=== added file 'pkg/bio/trimal/Makefile'
--- a/pkg/bio/trimal/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/trimal/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,55 @@
+# Copyright © 2013, 2014, 2015 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = trimAl
+GARNAME = trimal
+GARVERSION = 1.2rev59
+HOME_URL = http://trimal.cgenomics.org/
+DESCRIPTION = A tool for automated alignment trimming
+define BLURB
+trimAl is a tool for the automated removal of spurious sequences or
+poorly aligned regions from a multiple sequence alignment.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1093/bioinformatics/btp348
+
+######################################################################
+
+MASTER_SITES = http://trimal.cgenomics.org/
+MASTER_SUBDIR = _media/
+DISTNAME = $(UPSTREAMNAME).v$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/$(NAME)
+BUILD_SCRIPTS = $(WORKSRC)/source/makefile
+INSTALL_SCRIPTS = bins
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+BINS = readal trimal
+
+install-bins:
+ install -d $(packageprefix)/bin
+ for bin in $(BINS); do \
+ install -m 755 $(WORKSRC)/source/$$bin
$(packageprefix)/bin/$$bin; \
+ done
+ $(MAKECOOKIE)
=== added file 'pkg/bio/trimal/sha256sums'
--- a/pkg/bio/trimal/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/trimal/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+a29a3807e5a6c7a3d7e2185d8dd268415190a527668aaa04a4b42fc1f7db96fe
download/trimal.v1.2rev59.tar.gz
=== added directory 'pkg/bio/weeder'
=== added file 'pkg/bio/weeder/Makefile'
--- a/pkg/bio/weeder/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/weeder/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,63 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = Weeder
+GARNAME = weeder
+GARVERSION = 2.0
+HOME_URL = http://159.149.160.51/modtools/
+DESCRIPTION = Motif discovery in sequences from co-regulated genes
+define BLURB
+Weeder is a tool for transcription factor binding motif discovery from
+co-regulated genes of a single species. It has been optimized for
+ChIP-Seq data.
+endef
+LICENSE = GPLv3
+CITE = PMID:16845071
+
+######################################################################
+
+MASTER_SITES = http://159.149.160.51/
+MASTER_SUBDIR = modtools/downloads/
+DISTNAME = $(GARNAME)$(GARVERSION)
+DISTFILES = $(DISTNAME).tar.gz
+EXTRACTDIR = $(WORKSRC)
+BUILD_SCRIPTS = bin
+INSTALL_SCRIPTS = data bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+build-bin:
+ $(CXX) $(WORKSRC)/weeder2.cpp -o $(WORKSRC)/weeder2 -O3
+ $(MAKECOOKIE)
+
+install-data:
+ mkdir -p $(packageprefix)/share/weeder2/FreqFiles
+ for f in $(WORKSRC)/FreqFiles/*; do \
+ install -m644 $$f
$(packageprefix)/share/weeder2/FreqFiles/`basename $$f`; \
+ done
+ $(MAKECOOKIE)
+
+install-bin:
+ install -m755 $(WORKSRC)/weeder2 $(packageprefix)/share/weeder2/weeder2
+ $(SYMLINK_BIN) $(prefix)/share/weeder2/weeder2 weeder2
+ $(MAKECOOKIE)
=== added file 'pkg/bio/weeder/sha256sums'
--- a/pkg/bio/weeder/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/weeder/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+1bd21b26369a1cd90c59af3b94c9cacd516308231b27da9475af250b58b6ad33
download/weeder2.0.tar.gz
=== added directory 'pkg/bio/weederh'
=== added file 'pkg/bio/weederh/Makefile'
--- a/pkg/bio/weederh/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/weederh/Makefile 2016-06-17 19:57:40 +0000
@@ -0,0 +1,64 @@
+# Copyright © 2013, 2014 Brandon Invergo <address@hidden>
+#
+# This file is part of GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+NAME = WeederH
+GARNAME = weederh
+UPSTREAMNAME = weederH
+GARVERSION = 1.0
+HOME_URL = http://159.149.160.51/modtools/
+DESCRIPTION = Find conserved regulatory regions in homologous sequences
+define BLURB
+WeederH implements an algorithm for identifying conserved regulatory
+motifs and regions in homologous sequences.
+endef
+LICENSE = GPLv3
+CITE = doi:10.1186/1471-2105-8-46
+
+######################################################################
+
+MASTER_SITES = http://159.149.160.51/
+MASTER_SUBDIR = modtools/downloads/
+DISTNAME = $(UPSTREAMNAME)
+DISTFILES = $(DISTNAME).tar.gz
+WORKSRC = $(WORKDIR)/WeederH
+BUILD_SCRIPTS = bin
+INSTALL_SCRIPTS = data bin
+
+BUILDDEPS =
+LIBDEPS =
+
+######################################################################
+
+include ../../../gar/gar.mk
+include config.mk
+
+
+build-bin:
+ $(CC) $(WORKSRC)/weederH.c -o $(WORKSRC)/weederH -lm -O3
+ $(MAKECOOKIE)
+
+install-data:
+ mkdir -p $(packageprefix)/share/weederh/FreqH
+ for f in $(WORKSRC)/FreqH/*; do \
+ install -m644 $$f
$(packageprefix)/share/weederh/FreqH/`basename $$f`; \
+ done
+ $(MAKECOOKIE)
+
+install-bin:
+ install -m755 $(WORKSRC)/weederH $(packageprefix)/share/weederh/weederH
+ $(SYMLINK_BIN) $(prefix)/share/weederh/weederH weederH
+ $(MAKECOOKIE)
=== added file 'pkg/bio/weederh/sha256sums'
--- a/pkg/bio/weederh/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/weederh/sha256sums 2016-06-17 19:57:40 +0000
@@ -0,0 +1,1 @@
+d63422961ed1da651145c5236fec2f5fbb95f6b67dd22dc5059171b3e307922a
download/weederH.tar.gz
=== removed directory 'pkg/external/python2'
=== removed file 'pkg/external/python2/Makefile'
--- a/pkg/external/python2/Makefile 2016-06-17 19:08:15 +0000
+++ b/pkg/external/python2/Makefile 1970-01-01 00:00:00 +0000
@@ -1,10 +0,0 @@
-GARNAME = python
-GARVERSION = 2
-
-BINFILES=python2
-SIGFILES = $(DISTNAME).tar.gz.asc
-
-HOME_URL = http://www.python.org
-DESCRIPTION = interactive high-level object-oriented language
-
-include ../../gar.lib/external.mk
=== modified file 'pkg/other/libffi/Makefile'
--- a/pkg/other/libffi/Makefile 2016-06-17 06:43:09 +0000
+++ b/pkg/other/libffi/Makefile 2016-06-17 19:57:40 +0000
@@ -30,7 +30,8 @@
function specified by a call interface description at run-time.
endef
GARVERSION = 3.2.1
-LICENSE = see https://github.com/libffi/libffi/blob/master/LICENSE
+#LICENSE = see https://github.com/libffi/libffi/blob/master/LICENSE
+LICENSE = BSD
######################################################################
=== modified file 'pkg/other/libffi/config.mk'
--- a/pkg/other/libffi/config.mk 2016-06-17 07:22:39 +0000
+++ b/pkg/other/libffi/config.mk 2016-06-17 19:57:40 +0000
@@ -1,11 +1,4 @@
-<<<<<<< TREE
-## Configuration options ##
-
-CONFIGURE_OPTS ?=
-BUILD_OPTS ?=
-=======
## Configuration options ##
CONFIGURE_OPTS ?=
BUILD_OPTS ?=
->>>>>>> MERGE-SOURCE
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