[Gsrc-commit] trunk r8229: tophat adjust

[Carl Hansen]

------------------------------------------------------------
revno: 8229
revision-id: carlhansen1234@gmail.com-20220403064210-oa3ahmdm365g5dvb
parent: carlhansen1234@gmail.com-20220402214032-5xn8k57neppxmw8d
committer: carlhansen1234@gmail.com
branch nick: trunk
timestamp: Sat 2022-04-02 23:42:10 -0700
message:
  tophat adjust
modified:
  pkg/bio/tophat/Makefile        makefile-20160617195624-kwz1a09vkg4le6fu-193
  pkg/bio/tophat/sha256sums      sha256sums-20160617195624-kwz1a09vkg4le6fu-194

=== modified file 'pkg/bio/tophat/Makefile'
--- a/pkg/bio/tophat/Makefile   2016-06-17 19:57:40 +0000
+++ b/pkg/bio/tophat/Makefile   2022-04-03 06:42:10 +0000
@@ -1,6 +1,8 @@
 # Copyright © 2013, 2014 Brandon Invergo <brandon@invergo.net>
+# Copyright © 2022 Carl Hansen <carlhansen@gmail.com>
 #
-# This file is part of GSRC.
+# This file is part of GSRC, the GNU Source Release Collection.
+# http://www.gnu.org/software/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
@@ -14,20 +16,27 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with GSRC.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
 
 NAME = TopHat
 GARNAME = tophat
-GARVERSION = 2.0.11
+GARVERSION = 2.1.1
 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
+RNA-Seq reads to genomes using using Bowtie and then analyzes the results
+to identify splice junctions between exons "TopHat has entered a low
+maintenance, low support stage as it is now largely superseded by HISAT2
+which provides the same core functionality (i.e. spliced alignment of
+RNA-Seq reads), in a more accurate and much more efficient way."  
 endef
 LICENSE = Boost Software License 1.0
 CITE = doi:10.1093/bioinformatics/btp120
 
+
 ######################################################################
 
 MASTER_SITES = http://ccb.jhu.edu/
@@ -35,7 +44,7 @@
 DISTFILES = $(DISTNAME).tar.gz
 
 BUILDDEPS =
-LIBDEPS = python2 seqan samtools
+LIBDEPS = # python2 seqan samtools
 
 USE_AUTORECONF = y
 

=== modified file 'pkg/bio/tophat/sha256sums'
--- a/pkg/bio/tophat/sha256sums 2016-06-17 19:57:40 +0000
+++ b/pkg/bio/tophat/sha256sums 2022-04-03 06:42:10 +0000
@@ -1,1 +1,1 @@
-0498a9a7c6dd92a810e58902f422bc7d530de9014174cbb3f959ba776d5abf07  
download/tophat-2.0.11.tar.gz
+37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5  
download/tophat-2.1.1.tar.gz