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[Gsrc-commit] trunk r4429: unify gsrc biosrc
From: |
Carl Hansen |
Subject: |
[Gsrc-commit] trunk r4429: unify gsrc biosrc |
Date: |
Tue, 4 Apr 2017 23:14:41 -0400 (EDT) |
User-agent: |
Bazaar (2.7.0dev1) |
------------------------------------------------------------
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+this file is out of date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]
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Carl Hansen <=