[Gsrc-commit] trunk r4429: unify gsrc biosrc

[Carl Hansen]

------------------------------------------------------------
revno: 4429
revision-id: address@hidden
parent: address@hidden
committer: address@hidden
branch nick: trunk
timestamp: Tue 2017-04-04 20:14:23 -0700
message:
  unify gsrc biosrc
modified:
  TODO                           todo-20100608201528-d2g375z23moqiuaq-1

=== modified file 'TODO'
--- a/TODO      2014-10-06 19:15:32 +0000
+++ b/TODO      2017-04-05 03:14:23 +0000
@@ -13,6 +13,11 @@
 # process difficult or impossible.
 #
 # Note: this file is best viewed in Emacs Org-Mode
+#
+
+to do : learn org-mode
+
+this file is out of date
 
 * General tasks [0%]
 ** TODO Old tasks, pre-Brandon...to be reconsidered [88%]
@@ -1378,3 +1383,414 @@
 ** DONE webservices
    CLOSED: [2012-12-16 Sun 20:12]
 ** TODO wrappers
+# -*- org -*-
+#+TITLE: BioSRC TODO List
+#+AUTHOR: Brandon Invergo
+#+EMAIL: address@hidden
+#+DESCRIPTION: This file tracks all of the TODO items for BioSRC, primarily for
+#+DESCRIPTION: adding new packages but also for improvements to the system.
+#+TODO: TODO CANTADD ADDDEPS PROBLEM | DONE
+
+* System
+** DONE Add rule for checking for existence of upstream updates
+   CLOSED: [2014-05-21 Wed 11:58]
+* Packages
+** bio [53/134]
+*** CANTADD abyss
+    http://www.bcgsc.ca/platform/bioinfo/software/abyss
+    Has contradictory license terms: "GPL for non-commercial use"
+*** TODO arachne
+[[http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page]]
+*** TODO awty
+http://ceb.scs.fsu.edu/awty
+*** TODO axtchain
+http://genomewiki.ucsc.edu/index.php/The_source_tree
+http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
+http://genomewiki.cse.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
+The axtChain program is in the kent source tree:
+/kent/src/hg/mouseStuff/axtChain
+*** DONE bamtools
+    CLOSED: [2014-03-13 Thu 21:30]
+*** TODO bcftools
+http://sourceforge.net/projects/samtools/files/samtools/1.0/
+https://github.com/samtools/bcftools
+*** TODO beast
+https://code.google.com/p/beast-mcmc/
+*** TODO bedops
+https://github.com/bedops/bedops
+*** DONE bedtools
+    CLOSED: [2014-02-27 Thu 22:08]
+*** DONE bfast
+    CLOSED: [2014-03-13 Thu 21:38]
+*** DONE bismark
+    CLOSED: [2014-03-13 Thu 21:45]
+*** CANTADD blat
+    Academic-use-only license
+*** DONE bowtie
+    CLOSED: [2014-02-27 Thu 22:32]
+*** DONE breakway
+    CLOSED: [2014-03-13 Thu 22:02]
+*** DONE bwa
+    CLOSED: [2014-04-07 Mon 15:31]
+*** TODO cafe
+http://sites.bio.indiana.edu/~hahnlab/Software.html
+*** TODO ccat
+http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm
+*** DONE cd-hit
+    CLOSED: [2014-07-21 Mon 18:12]
+*** TODO cegma
+http://korflab.ucdavis.edu/Datasets/cegma/
+*** DONE clustal-omega
+    CLOSED: [2014-02-24 Mon 10:34]
+*** DONE clustalw
+    CLOSED: [2014-02-24 Mon 10:34]
+*** TODO consed
+http://www.phrap.org/phredphrapconsed.html#block_consed
+*** TODO coseg
+http://www.repeatmasker.org/COSEGDownload.html
+*** DONE csblast
+    CLOSED: [2014-07-17 Thu 15:53]
+*** DONE cufflinks
+    CLOSED: [2014-02-27 Thu 23:18]
+*** TODO cutadapt
+https://code.google.com/p/cutadapt/
+*** DONE dnaa
+    CLOSED: [2014-04-07 Mon 17:00]
+*** TODO dnasp
+http://www.ub.edu/dnasp/
+*** TODO dustmasker
+https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker
+*** DONE e-pcr
+    CLOSED: [2014-04-08 Tue 15:10]
+*** PROBLEM eautils
+    https://code.google.com/p/ea-utils/
+    Uses Google Drive to distribute files, so no direct download link
+    Use SVN checkout (no tags available for releases)
+*** DONE emboss
+    CLOSED: [2014-02-24 Mon 14:40]
+*** TODO eponine
+https://www.sanger.ac.uk/resources/software/eponine/
+*** TODO exonerate
+https://www.ebi.ac.uk/~guy/exonerate/
+*** TODO fastcodeml
+*** TODO fastqc
+    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+    GPL
+    Check if can be built without GUI
+*** DONE fasttree
+    CLOSED: [2014-02-24 Mon 15:08]
+*** DONE fastx-toolkit
+    CLOSED: [2014-02-28 Fri 10:40]
+*** CANTADD foldx
+    proprietary; no source or executable freely available
+*** DONE fsa
+    CLOSED: [2014-02-24 Mon 15:22]
+*** TODO fundi
+*** TODO gphocs
+http://compgen.bscb.cornell.edu/GPhoCS/
+*** TODO gatk
+https://www.broadinstitute.org/gatk/
+*** TODO garli
+https://www.nescent.org/wg_garli/Main_Page
+*** CANTADD gblocks
+    Proprietary (no source, no license)
+*** TODO glfprogs
+http://maq.sourceforge.net/glfProgs.shtml
+*** TODO hapsembler
+http://compbio.cs.toronto.edu/hapsembler/
+*** DONE hmmer
+    CLOSED: [2014-02-19 Wed 20:15]
+*** DONE hyphy
+    CLOSED: [2014-03-03 Mon 16:12]
+*** TODO interproscan
+    https://code.google.com/p/interproscan/
+    Apache license
+*** TODO ispcr
+http://users.soe.ucsc.edu/~kent/src/
+in-silico pcr
+*** CANTADD iupred
+    proprietary
+*** DONE jellyfish
+    CLOSED: [2014-05-23 Fri 18:15]
+    http://www.genome.umd.edu/jellyfish.html
+*** TODO jmodeltest2
+https://code.google.com/p/jmodeltest2/
+*** DONE kraken
+    CLOSED: [2014-05-23 Fri 18:34]
+    http://ccb.jhu.edu/software/kraken/
+*** TODO lastz
+http://www.bx.psu.edu/~rsharris/lastz/
+*** DONE macs
+    CLOSED: [2014-03-05 Wed 22:19]
+*** DONE mafft
+    CLOSED: [2014-02-24 Mon 16:24]
+*** TODO maq
+http://maq.sourceforge.net/maq-man.shtml
+*** CANTADD mega
+    Proprietary license (and not available for GNU/Linux?)
+*** DONE melting
+    CLOSED: [2014-02-19 Wed 20:15]
+*** CANTADD meme
+    http://meme.ebi.edu.au/meme/intro.html
+    Restrictive (academic-only) license
+*** CANTADD modeller
+    proprietary
+*** CANTADD modpipe
+    free software, but has a hard dependency on Modeller
+*** TODO monocle
+http://monocle-bio.sourceforge.net/
+*** DONE moods
+    CLOSED: [2014-03-05 Wed 22:49]
+*** DONE mrbayes
+    CLOSED: [2014-03-06 Thu 20:21]
+*** TODO mrfast
+http://sourceforge.net/projects/mrfast/
+*** TODO mrsfast
+http://mrsfast.sourceforge.net/Home
+*** TODO ms
+http://home.uchicago.edu/~rhudson1/source/mksamples.html
+*** TODO multiz
+http://www.bx.psu.edu/miller_lab/
+*** DONE mummer
+    CLOSED: [2014-04-07 Mon 16:01]
+*** CANTADD muscle
+    proprietary (no license available)
+*** DONE ncbi-blast
+    CLOSED: [2014-02-24 Mon 10:34]
+*** DONE newick-utils
+    CLOSED: [2014-02-24 Mon 11:03]
+*** DONE oma
+    CLOSED: [2014-02-19 Wed 20:49]
+*** ADDDEPS pagan-msa
+    boost
+*** CANTADD paml
+    restrictive academic-use-only clause
+*** CANTADD paup
+    proprietary?
+    http://paup.csit.fsu.edu/
+*** ADDDEPS pfamscan
+*** TODO phast
+http://compgen.bscb.cornell.edu/phast/
+*** TODO phrap
+http://www.phrap.org/phredphrapconsed.html#block_phrap
+*** TODO phred
+http://www.phrap.org/phredphrapconsed.html#block_phred
+*** CANTADD phylip
+    Restrictive license (can't use commercially)
+*** TODO picard
+    http://picard.sourceforge.net/
+*** TODO pinstripe
+    http://pinstripe.matticklab.com/
+*** DONE phyml
+    CLOSED: [2014-02-24 Mon 11:35]
+*** DONE primer3
+    CLOSED: [2014-04-07 Mon 15:45]
+*** DONE prank-msa
+    CLOSED: [2014-02-24 Mon 11:23]
+*** PROBLEM prottest
+    https://code.google.com/p/prottest3/
+    Uses Google Drive to distribute files, so no direct download.
+    Use Hg checkout?
+*** DONE provean
+    CLOSED: [2014-07-22 Tue 12:28]
+    http://provean.jcvi.org/index.php
+    GPLv3
+*** DONE pscan
+    CLOSED: [2014-05-23 Fri 18:47]
+*** TODO psmc
+*** DONE qmmraxml
+    CLOSED: [2014-02-26 Wed 22:57]
+*** DONE quake
+    CLOSED: [2014-04-07 Mon 13:44]
+*** TODO quicktree
+https://www.sanger.ac.uk/resources/software/quicktree/
+*** DONE raxml
+    CLOSED: [2014-02-19 Wed 22:25]
+*** TODO repeatmasker
+http://www.repeatmasker.org/
+*** DONE reapr
+    CLOSED: [2014-04-07 Mon 15:24]
+*** CANTADD rnaprofile
+    No license
+*** DONE rnaz
+    CLOSED: [2014-04-07 Mon 15:52]
+*** DONE samtoools
+    CLOSED: [2014-02-27 Thu 23:11]
+*** DONE seqsuite
+    CLOSED: [2014-02-24 Mon 16:25]
+*** DONE seqtk
+    CLOSED: [2014-06-23 Mon 22:43]
+    https://github.com/lh3/seqtk
+*** CANTADD sift
+    Restrictive license (non-commercial)
+*** TODO sff2fastq
+    https://github.com/indraniel/sff2fastq
+    no official release...
+*** TODO slimcodeml
+*** DONE slimsuite
+    CLOSED: [2014-09-19 Fri 14:35]
+*** DONE smalt
+    CLOSED: [2014-06-26 Thu 19:20]
+    https://www.sanger.ac.uk/resources/software/smalt/
+*** TODO snpeff
+    http://sourceforge.net/projects/snpeff/
+*** DONE snpomatic
+    CLOSED: [2014-04-07 Mon 14:17]
+*** TODO soapdenovo
+    http://soap.genomics.org.cn/
+*** TODO soapaligner/soap2
+    http://soap.genomics.org.cn/
+*** TODO soapsplice
+    http://soap.genomics.org.cn/
+*** TODO soapsnp
+    http://soap.genomics.org.cn/
+*** TODO soapindel
+    http://soap.genomics.org.cn/
+*** TODO soapsv
+    http://soap.genomics.org.cn/
+*** TODO sra-toolkit
+    https://www.ncbi.nlm.nih.gov/Traces/sra/?view=software
+    Massive pain to build...try again some other time    
+*** TODO srma
+    http://sourceforge.net/projects/srma/
+*** TODO ssaha2
+    https://www.sanger.ac.uk/resources/software/ssaha2/
+*** TODO stampy
+*** DONE t-coffee
+    CLOSED: [2014-02-19 Wed 20:16]
+*** DONE tabix
+    CLOSED: [2014-04-07 Mon 14:08]
+*** TODO tdg09
+    https://github.com/tamuri/tdg09
+*** TODO tdg12
+    https://github.com/tamuri/tdg12
+*** TODO tophat
+    http://tophat.cbcb.umd.edu/
+    Boost, probably, like cufflinks
+*** DONE treebest
+    CLOSED: [2014-04-02 Wed 14:02]
+*** TODO treesoft
+http://sourceforge.net/projects/treesoft/
+*** DONE trimal
+    CLOSED: [2014-02-19 Wed 21:08]
+*** TODO trinity
+    http://trinityrnaseq.sourceforge.net/
+    BSD
+*** TODO velvet
+    https://www.ebi.ac.uk/~zerbino/velvet/
+*** TODO viennarna
+    http://www.tbi.univie.ac.at/~ronny/RNA/
+*** DONE weeder
+    CLOSED: [2014-05-23 Fri 18:57]
+    GPLv3
+*** DONE weederh
+    CLOSED: [2014-05-23 Fri 19:09]
+** dev [3/7]
+*** TODO apache-ant
+    dep of melting
+*** DONE gcc
+    CLOSED: [2014-05-14 Wed 12:38]
+*** TODO lua
+*** TODO perl
+*** DONE python
+    CLOSED: [2014-03-03 Mon 14:18]
+*** DONE python2
+    CLOSED: [2014-03-03 Mon 14:47]
+*** TODO ruby
+** libs [20/33]
+*** DONE bambamc
+    CLOSED: [2014-06-26 Thu 19:18]
+    https://github.com/gt1/bambamc
+*** DONE glpk
+    CLOSED: [2014-02-19 Wed 20:17]
+*** TODO gmp
+*** DONE gsl
+    CLOSED: [2014-02-19 Wed 20:17]
+*** DONE beagle-lib
+    CLOSED: [2014-03-06 Thu 20:06]
+*** TODO boost
+    dep of pagan-msa
+*** DONE eigen
+    CLOSED: [2014-02-27 Thu 23:11]
+*** DONE gdbm
+    CLOSED: [2014-03-05 Wed 15:45]
+*** DONE htslib
+    CLOSED: [2014-09-19 Fri 14:34]
+*** DONE libgtextutils
+    CLOSED: [2014-02-28 Fri 10:41]
+*** TODO mpc
+*** TODO mpfr
+*** DONE perl-bioperl
+    CLOSED: [2014-02-19 Wed 20:17]
+*** TODO perl-ensembl
+*** TODO perl-moose [0/22]
+    pre-req for pfamscan
+**** TODO perl-class-load
+**** TODO perl-class-load-xs
+**** TODO perl-data-optlist
+**** TODO perl-devel-globaldestruction
+**** TODO perl-dist-checkconflicts
+**** TODO perl-eval-closure
+**** TODO perl-list-moreutils
+**** TODO perl-mro-compat
+**** TODO perl-package-deprecationmanager
+**** TODO perl-package-stash
+**** TODO perl-package-stash-xs
+**** TODO perl-params-util
+**** TODO perl-sub-exporter
+**** TODO perl-sub-name
+**** TODO perl-task-weaken
+**** TODO perl-test-checkdeps
+**** TODO perl-try-tiny
+**** TODO perl-devel-stacktrace
+**** TODO perl-dist-checkconflicts
+**** TODO perl-test-fatal
+**** TODO perl-test-requires
+**** TODO perl-test-without-module
+*** DONE python-biopython
+    CLOSED: [2014-02-19 Wed 20:17]
+*** DONE python-dateutil
+    CLOSED: [2014-05-14 Wed 11:27]
+*** DONE python-htseq
+    CLOSED: [2014-02-28 Fri 11:01]
+*** TODO python-matplotlib
+*** DONE python-networkx
+    CLOSED: [2014-03-06 Thu 10:50]
+*** TODO python-nose
+*** DONE python-numpy
+    CLOSED: [2014-03-05 Wed 15:34]
+*** DONE python-pandas
+    CLOSED: [2014-05-14 Wed 11:26]
+*** TODO python-pybedtools
+https://pypi.python.org/pypi/pybedtools
+*** TODO python-pycogent
+*** TODO python-scikit-learn
+*** DONE python-scipy
+    CLOSED: [2014-03-05 Wed 15:34]
+*** DONE python-setuptools
+    CLOSED: [2014-04-23 Wed 17:09]
+*** DONE python-sqlalchemy
+    CLOSED: [2014-04-23 Wed 17:09]
+*** TODO python-sympy
+*** TODO r-cummerbund
+http://compbio.mit.edu/cummeRbund/
+*** DONE seqan
+    CLOSED: [2014-06-26 Thu 23:04]
+*** DONE sparsehash
+    CLOSED: [2014-07-17 Thu 14:14]
+** tools [7/8]
+*** DONE datamash
+    CLOSED: [2014-05-21 Wed 22:46]
+*** TODO ipython
+*** DONE mcsim
+    CLOSED: [2014-02-19 Wed 20:18]
+*** DONE parallel
+    CLOSED: [2014-02-26 Wed 22:31]
+*** DONE plotutils
+    CLOSED: [2014-02-19 Wed 20:18]
+*** DONE units
+    CLOSED: [2014-02-19 Wed 20:18]
+*** DONE wdiff
+    CLOSED: [2014-02-19 Wed 20:18]
+*** DONE zeptodb
+    CLOSED: [2014-02-26 Wed 22:31]