[Gsrc-commit] trunk r4431: out of date

[Carl Hansen]

------------------------------------------------------------
revno: 4431
revision-id: address@hidden
parent: address@hidden
committer: Carl Hansen <address@hidden>
branch nick: trunk
timestamp: Wed 2017-04-05 10:36:58 -0700
message:
  out of date
removed:
  TODO.biosrc.org                
todo.biosrc.org-20160617190624-gewvabotlg7zvguu-1

=== removed file 'TODO.biosrc.org'
--- a/TODO.biosrc.org   2016-06-17 19:08:15 +0000
+++ b/TODO.biosrc.org   1970-01-01 00:00:00 +0000
@@ -1,411 +0,0 @@
-# -*- 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]