Changeset [521b70151572cdbc99392cae2a94649cbaf52c79] by Mark Fiers

Revision 521b70151572cdbc99392cae2a94649cbaf52c79, committed by Mark Fiers · October 22nd, 2012 @ 08:48 PM

merged
https://github.com/mfiers/Moa/commit/521b70151572cdbc99392cae2a9464...

464 changed files

A bin/fastq2contigs
A bin/moa_template_setup
A lib/jinja2/template.readme.jinja2
A lib/python/moa/cli.py
A lib/python/moa/plugin/job/versioning.py
A lib/python/moa/plugin/system/doc/__init__.py
A lib/python/moa/plugin/system/doc/pelican_util.py
A lib/python/moa/plugin/system/doc/templates/file.page.jinja2
A lib/python/moa/plugin/system/doc/templates/parameter.page.jinja2
A lib/python/moa/plugin/system/doc/templates/pelican.conf.jinja2
A lib/python/moa/plugin/system/doc/templates/redirect.jinja2
A lib/python/moa/plugin/system/doc/templates/template.page.jinja2
A lib/python/moa/plugin/system/doc/templates/versioning.page.jinja2
A lib/python/moa/plugin/system/doc/theme/LICENSE.txt
A lib/python/moa/plugin/system/doc/theme/NOTICE.txt
A lib/python/moa/plugin/system/doc/theme/static/bootstrap.min.css
A lib/python/moa/plugin/system/doc/theme/static/forkme_right_darkblue_121621.png
A lib/python/moa/plugin/system/doc/theme/static/html5.js
A lib/python/moa/plugin/system/doc/theme/static/images/icons/activestate.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/bitbucket.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/delicious.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/favicon.ico
A lib/python/moa/plugin/system/doc/theme/static/images/icons/github.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/jamendo.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/lastfm.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/linkedin.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/phosting.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/reader.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/rss.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/stackoverflow.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/twitter.png
A lib/python/moa/plugin/system/doc/theme/static/images/icons/weibo.png
A lib/python/moa/plugin/system/doc/theme/static/images/moa.logo.very.small.png
A lib/python/moa/plugin/system/doc/theme/static/local.css
A lib/python/moa/plugin/system/doc/theme/static/pygments.css
A lib/python/moa/plugin/system/doc/theme/templates/analytics.html
A lib/python/moa/plugin/system/doc/theme/templates/archives.html
A lib/python/moa/plugin/system/doc/theme/templates/article.html
A lib/python/moa/plugin/system/doc/theme/templates/author.html
A lib/python/moa/plugin/system/doc/theme/templates/base.html
A lib/python/moa/plugin/system/doc/theme/templates/categories.html
A lib/python/moa/plugin/system/doc/theme/templates/category.html
A lib/python/moa/plugin/system/doc/theme/templates/disqus.html
A lib/python/moa/plugin/system/doc/theme/templates/facebook.html
A lib/python/moa/plugin/system/doc/theme/templates/github.html
A lib/python/moa/plugin/system/doc/theme/templates/index.html
A lib/python/moa/plugin/system/doc/theme/templates/metadata.html
A lib/python/moa/plugin/system/doc/theme/templates/page.html
A lib/python/moa/plugin/system/doc/theme/templates/tag.html
A lib/python/moa/plugin/system/doc/theme/templates/tags.html
A lib/python/moa/plugin/system/doc/theme/templates/twitter.html
A lib/python/moa/template/local_templates/abyss_pe.jinja2
A lib/python/moa/template/local_templates/abyss_pe.moa
A lib/python/moa/template/local_templates/abyss_se.jinja2
A lib/python/moa/template/local_templates/abyss_se.moa
A lib/python/moa/template/local_templates/archroot.jinja2
A lib/python/moa/template/local_templates/archroot.moa
A lib/python/moa/template/local_templates/bamextract.jinja2
A lib/python/moa/template/local_templates/bamextract.moa
A lib/python/moa/template/local_templates/bdbb.jinja2
A lib/python/moa/template/local_templates/bdbb.moa
A lib/python/moa/template/local_templates/bfast_aln.jinja2
A lib/python/moa/template/local_templates/bfast_aln.moa
A lib/python/moa/template/local_templates/bfast_db.jinja2
A lib/python/moa/template/local_templates/bfast_db.moa
A lib/python/moa/template/local_templates/blast.jinja2
A lib/python/moa/template/local_templates/blast.moa
A lib/python/moa/template/local_templates/blastdb.jinja2
A lib/python/moa/template/local_templates/blastdb.moa
A lib/python/moa/template/local_templates/bowtie.jinja2
A lib/python/moa/template/local_templates/bowtie.moa
A lib/python/moa/template/local_templates/bowtie_pe.finish.jinja2
A lib/python/moa/template/local_templates/bowtie_pe.jinja2
A lib/python/moa/template/local_templates/bowtie_pe.moa
A lib/python/moa/template/local_templates/bowtie_se.jinja2
A lib/python/moa/template/local_templates/bowtie_se.moa
A lib/python/moa/template/local_templates/bowtiedb.jinja2
A lib/python/moa/template/local_templates/bowtiedb.moa
A lib/python/moa/template/local_templates/bwa_aln.jinja2
A lib/python/moa/template/local_templates/bwa_aln.moa
A lib/python/moa/template/local_templates/bwa_index.jinja2
A lib/python/moa/template/local_templates/bwa_index.moa
A lib/python/moa/template/local_templates/bwa_sampe.jinja2
A lib/python/moa/template/local_templates/bwa_sampe.moa
A lib/python/moa/template/local_templates/bwa_samse.jinja2
A lib/python/moa/template/local_templates/bwa_samse.moa
A lib/python/moa/template/local_templates/cdsmatrix.jinja2
A lib/python/moa/template/local_templates/cdsmatrix.moa
A lib/python/moa/template/local_templates/empty.jinja2
A lib/python/moa/template/local_templates/empty.moa
A lib/python/moa/template/local_templates/fastainfo.finish.py
A lib/python/moa/template/local_templates/fastainfo.moa
A lib/python/moa/template/local_templates/fastainfo.run.py
A lib/python/moa/template/local_templates/fastqc.jinja2
A lib/python/moa/template/local_templates/fastqc.moa
A lib/python/moa/template/local_templates/fastx_clipper.jinja2
A lib/python/moa/template/local_templates/fastx_clipper.moa
A lib/python/moa/template/local_templates/fastx_qual_stats.jinja2
A lib/python/moa/template/local_templates/fastx_qual_stats.moa
A lib/python/moa/template/local_templates/filterwgs_pair.jinja2
A lib/python/moa/template/local_templates/filterwgs_pair.moa
A lib/python/moa/template/local_templates/genemarks.jinja2
A lib/python/moa/template/local_templates/genemarks.moa
A lib/python/moa/template/local_templates/glimmer3.jinja2
A lib/python/moa/template/local_templates/glimmer3.moa
A lib/python/moa/template/local_templates/gmap.jinja2
A lib/python/moa/template/local_templates/gmap.moa
A lib/python/moa/template/local_templates/gmapdb.jinja2
A lib/python/moa/template/local_templates/gmapdb.moa
A lib/python/moa/template/local_templates/gsMapper.jinja2
A lib/python/moa/template/local_templates/hagfish.jinja2
A lib/python/moa/template/local_templates/hagfish.moa
A lib/python/moa/template/local_templates/kanga.jinja2
A lib/python/moa/template/local_templates/kanga.moa
A lib/python/moa/template/local_templates/kangar_pe.jinja2
A lib/python/moa/template/local_templates/kangar_pe.moa
A lib/python/moa/template/local_templates/kangar_se.jinja2
A lib/python/moa/template/local_templates/kangar_se.moa
A lib/python/moa/template/local_templates/kangax.jinja2
A lib/python/moa/template/local_templates/kangax.moa
A lib/python/moa/template/local_templates/map.jinja2
A lib/python/moa/template/local_templates/map.moa
A lib/python/moa/template/local_templates/map2.jinja2
A lib/python/moa/template/local_templates/map2.moa
A lib/python/moa/template/local_templates/map22.jinja2
A lib/python/moa/template/local_templates/map22.moa
A lib/python/moa/template/local_templates/maq_pe.jinja2
A lib/python/moa/template/local_templates/maq_pe.moa
A lib/python/moa/template/local_templates/maq_se.jinja2
A lib/python/moa/template/local_templates/maq_se.moa
A lib/python/moa/template/local_templates/mummer.jinja2
A lib/python/moa/template/local_templates/mummer.moa
A lib/python/moa/template/local_templates/ncbi.jinja2
A lib/python/moa/template/local_templates/ncbi.moa
A lib/python/moa/template/local_templates/orthomcl.jinja2
A lib/python/moa/template/local_templates/orthomcl.moa
A lib/python/moa/template/local_templates/orthomcl.tables.py
A lib/python/moa/template/local_templates/project.jinja2
A lib/python/moa/template/local_templates/project.moa
A lib/python/moa/template/local_templates/recursive_map.jinja2
A lib/python/moa/template/local_templates/recursive_map.moa
A lib/python/moa/template/local_templates/reduce.jinja2
A lib/python/moa/template/local_templates/reduce.moa
A lib/python/moa/template/local_templates/samtools_pileup.jinja2
A lib/python/moa/template/local_templates/samtools_pileup.moa
A lib/python/moa/template/local_templates/simple.jinja2
A lib/python/moa/template/local_templates/simple.moa
A lib/python/moa/template/local_templates/smalt_pe.jinja2
A lib/python/moa/template/local_templates/smalt_pe.moa
A lib/python/moa/template/local_templates/smaltdb.jinja2
A lib/python/moa/template/local_templates/smaltdb.moa
A lib/python/moa/template/local_templates/soapdenovo_pe.jinja2
A lib/python/moa/template/local_templates/soapdenovo_pe.moa
A lib/python/moa/template/local_templates/soapdenovo_postprocess.jinja2
A lib/python/moa/template/local_templates/soapdenovo_postprocess.moa
A lib/python/moa/template/local_templates/statsidx.jinja2
A lib/python/moa/template/local_templates/statsidx.moa
A lib/python/moa/template/local_templates/sync.jinja2
A lib/python/moa/template/local_templates/sync.moa
A lib/python/moa/template/local_templates/sync.run.py
A lib/python/moa/template/local_templates/unittest.jinja2
A lib/python/moa/template/local_templates/unittest.moa
A lib/python/moa/template/local_templates/wget.jinja2
A lib/python/moa/template/local_templates/wget.moa
A lib/python/moa/template/provider/gitmodule.py
A share/logo/moa.logo.very.small.xcf
A sphinx/api/args.rst
A sphinx/api/cli.rst
A sphinx/api/exceptions.rst
A sphinx/api/filesets.rst
A sphinx/api/logger.rst
A sphinx/api/version.rst
A sphinx/git.rst
A sphinx/templates/abyss_pe.rst
A sphinx/templates/abyss_se.rst
A sphinx/templates/archroot.rst
A sphinx/templates/bamextract.rst
A sphinx/templates/bdbb.rst
A sphinx/templates/bfast_aln.rst
A sphinx/templates/bfast_db.rst
A sphinx/templates/blast.rst
A sphinx/templates/blastdb.rst
A sphinx/templates/bowtie.rst
A sphinx/templates/bowtie_pe.rst
A sphinx/templates/bowtie_se.rst
A sphinx/templates/bowtiedb.rst
A sphinx/templates/bwa_aln.rst
A sphinx/templates/bwa_index.rst
A sphinx/templates/bwa_sampe.rst
A sphinx/templates/bwa_samse.rst
A sphinx/templates/cdsmatrix.rst
A sphinx/templates/empty.rst
A sphinx/templates/fastainfo.rst
A sphinx/templates/fastqc.rst
A sphinx/templates/fastx_clipper.rst
A sphinx/templates/fastx_qual_stats.rst
A sphinx/templates/filterwgs_pair.rst
A sphinx/templates/genemarks.rst
A sphinx/templates/glimmer3.rst
A sphinx/templates/gmap.rst
A sphinx/templates/gmapdb.rst
A sphinx/templates/hagfish.rst
A sphinx/templates/index.rst
A sphinx/templates/kanga.rst
A sphinx/templates/kangar_pe.rst
A sphinx/templates/kangar_se.rst
A sphinx/templates/kangax.rst
A sphinx/templates/map.rst
A sphinx/templates/map2.rst
A sphinx/templates/map22.rst
A sphinx/templates/maq_pe.rst
A sphinx/templates/maq_se.rst
A sphinx/templates/mummer.rst
A sphinx/templates/ncbi.rst
A sphinx/templates/newjobtest.rst
A sphinx/templates/orthomcl.rst
A sphinx/templates/project.rst
A sphinx/templates/recursive_map.rst
A sphinx/templates/reduce.rst
A sphinx/templates/samtools_pileup.rst
A sphinx/templates/simple.rst
A sphinx/templates/smalt_pe.rst
A sphinx/templates/smaltdb.rst
A sphinx/templates/soapdenovo_pe.rst
A sphinx/templates/soapdenovo_postprocess.rst
A sphinx/templates/statsidx.rst
A sphinx/templates/sync.rst
A sphinx/templates/unittest.rst
A sphinx/templates/wget.rst
A template2
A test/run_tests.sh
A test/scripts/commands/moa.sh
R jinja2/README
R lib/python/moa/plugin/system/doc.py
R lib/python/moa/plugin/system/metavar.py
R lib/python/moa/plugin/system/test.py
R template2/abyss_pe.jinja2
R template2/abyss_pe.moa
R template2/abyss_se.jinja2
R template2/abyss_se.moa
R template2/archroot.jinja2
R template2/archroot.moa
R template2/bamextract.jinja2
R template2/bamextract.moa
R template2/bdbb.jinja2
R template2/bdbb.moa
R template2/bfast_aln.jinja2
R template2/bfast_aln.moa
R template2/bfast_db.jinja2
R template2/bfast_db.moa
R template2/blast.jinja2
R template2/blast.moa
R template2/blastdb.jinja2
R template2/blastdb.moa
R template2/bowtie.jinja2
R template2/bowtie.moa
R template2/bowtie_pe.finish.jinja2
R template2/bowtie_pe.jinja2
R template2/bowtie_pe.moa
R template2/bowtie_se.jinja2
R template2/bowtie_se.moa
R template2/bowtiedb.jinja2
R template2/bowtiedb.moa
R template2/bwa_aln.moa
R template2/bwa_index.jinja2
R template2/bwa_index.moa
R template2/bwa_sampe.jinja2
R template2/bwa_sampe.moa
R template2/bwa_samse.jinja2
R template2/bwa_samse.moa
R template2/cdsmatrix.jinja2
R template2/cdsmatrix.moa
R template2/empty.jinja2
R template2/empty.moa
R template2/fastainfo.finish.py
R template2/fastainfo.moa
R template2/fastainfo.run.py
R template2/fastqc.jinja2
R template2/fastqc.moa
R template2/fastx_clipper.jinja2
R template2/fastx_clipper.moa
R template2/fastx_qual_stats.jinja2
R template2/fastx_qual_stats.moa
R template2/filterwgs_pair.jinja2
R template2/filterwgs_pair.moa
R template2/genemarks.moa
R template2/glimmer3.jinja2
R template2/glimmer3.moa
R template2/gmap.jinja2
R template2/gmap.moa
R template2/gmapdb.jinja2
R template2/gmapdb.moa
R template2/gsMapper.jinja2
R template2/hagfish.jinja2
R template2/hagfish.moa
R template2/kanga.jinja2
R template2/kanga.moa
R template2/kangar_pe.jinja2
R template2/kangar_pe.moa
R template2/kangar_se.jinja2
R template2/kangar_se.moa
R template2/kangax.jinja2
R template2/kangax.moa
R template2/map.jinja2
R template2/map.moa
R template2/map2.jinja2
R template2/map2.moa
R template2/map22.jinja2
R template2/map22.moa
R template2/maq_pe.jinja2
R template2/maq_pe.moa
R template2/maq_se.jinja2
R template2/maq_se.moa
R template2/mummer.jinja2
R template2/mummer.moa
R template2/ncbi.jinja2
R template2/ncbi.moa
R template2/orthomcl.jinja2
R template2/orthomcl.moa
R template2/orthomcl.tables.py
R template2/project.jinja2
R template2/project.moa
R template2/recursive_map.jinja2
R template2/recursive_map.moa
R template2/reduce.jinja2
R template2/reduce.moa
R template2/samtools_pileup.jinja2
R template2/samtools_pileup.moa
R template2/simple.moa
R template2/smalt_pe.jinja2
R template2/smalt_pe.moa
R template2/smaltdb.jinja2
R template2/smaltdb.moa
R template2/soapdenovo_pe.jinja2
R template2/soapdenovo_pe.moa
R template2/soapdenovo_postprocess.jinja2
R template2/soapdenovo_postprocess.moa
R template2/statsidx.jinja2
R template2/statsidx.moa
R template2/sync.jinja2
R template2/sync.moa
R template2/sync.run.py
R template2/unittest.jinja2
R template2/unittest.moa
R template2/wget.jinja2
R template2/wget.moa
R lib/ruff/snippets.jinja2
R sphinx/api/backend/gnumake.rst
R template2/adhoc.mk
R template2/adhoc.moa
R template2/bamextract.mk
R template2/bartab.mk
R template2/bartab.moa
R template2/blat.mk
R template2/blat.moa
R template2/bwa_aln.jinja2
R template2/cleanFasta.mk
R template2/cleanFasta.moa
R template2/clustalgroup.mk
R template2/clustalgroup.moa
R template2/clustalpair.mk
R template2/clustalpair.moa
R template2/clustalw.mk
R template2/clustalw.moa
R template2/concatenate.mk
R template2/concatenate.moa
R template2/dottup.mk
R template2/dottup.moa
R template2/fasta2gff.mk
R template2/fasta2gff.moa
R template2/gather.mk
R template2/gather.moa
R template2/genemarks.jinja2
R template2/getorf.mk
R template2/getorf.moa
R template2/glimmer3.mk
R template2/gmap.mk
R template2/gsMapper.mk
R template2/gsMapper.moa
R template2/h_blast.mk
R template2/h_blast.moa
R template2/lftp.mk
R template2/lftp.moa
R template2/maq_fasta2bfa.mk
R template2/maq_fasta2bfa.moa
R template2/maq_fastq2bfq.mk
R template2/maq_fastq2bfq.moa
R template2/maq_match_pair.mk
R template2/maq_match_pair.moa
R template2/moatest.mk
R template2/moatest.moa
R template2/ncbi.mk
R template2/newbler.mk
R template2/newbler.moa
R template2/nstretch.mk
R template2/nstretch.moa
R template2/pregap.mk
R template2/pregap.moa
R template2/sam2bam.mk
R template2/sam2bam.moa
R template2/sffinfo.mk
R template2/sffinfo.moa
R template2/simple.jinja2
R template2/varscan.mk
R template2/varscan.moa
R template2/vpcr.mk
R template2/vpcr.moa
R template2/vpcr_list.mk
R template2/vpcr_list.moa
R test/scripts/moa.sh
M Changelog.txt
M MANIFEST.in
M README
M VERSION
M bin/moa
M etc/config
M lib/python/Yaco/__init__.py
M lib/python/fist/__init__.py
M lib/python/fist/setup.py
M lib/python/moa/args.py
M lib/python/moa/backend/ruff/test.py
M lib/python/moa/job.py
M lib/python/moa/jobConf.py
M lib/python/moa/logger.py
M lib/python/moa/plugin/__init__.py
M lib/python/moa/plugin/job/completion.py
M lib/python/moa/plugin/job/metavar.py
M lib/python/moa/plugin/job/smw/__init__.py
M lib/python/moa/plugin/system/adhoc.py
M lib/python/moa/plugin/system/fileset.py
M lib/python/moa/plugin/system/info.py
M lib/python/moa/plugin/system/logger.py
M lib/python/moa/plugin/system/moaGit.py
M lib/python/moa/plugin/system/moautil.py
M lib/python/moa/plugin/system/newjob.py
M lib/python/moa/plugin/system/project.py
M lib/python/moa/plugin/system/template.py
M lib/python/moa/resources.py
M lib/python/moa/sysConf.py
M lib/python/moa/template/__init__.py
M lib/python/moa/template/provider/__init__.py
M lib/python/moa/template/provider/archive.py
M lib/python/moa/template/provider/core.py
M lib/python/moa/template/provider/local.py
M lib/python/moa/template/template.py
M lib/python/moa/utils.py
M setup.py
M sphinx/api/index.rst
M sphinx/api/plugin/index.rst
M sphinx/commands/index.rst
M sphinx/commands/update_commands
M sphinx/index.rst
M sphinx/install.rst
M sphinx/templates/refresh_templates
M test/scripts/commands/map.sh
M test/scripts/commands/set.sh
M test/scripts/commands/show.sh
M test/scripts/commands/simple.sh
M test/scripts/commands/unset.sh
M test/scripts/configure/00.main.sh
M test/test_doctest.py
M test/test_scripts.py
M test/test_templates.py
M util/newVersion