https://github.com/genome/genome
Tip revision: dde1f5fea559d20cbc39a8c2a31e8ee9f1a47b7a authored by Malachi Griffith on 06 February 2014, 03:53:02 UTC
fix documentation and other minor details related to installation of file based dbs from github
fix documentation and other minor details related to installation of file based dbs from github
Tip revision: dde1f5f
.gitmodules
[submodule "somatic-sniper"]
path = somatic-sniper
url = ssh://git/srv/git/somatic-sniper.git
[submodule "joinx"]
path = joinx
url = ssh://git/srv/git/joinx.git
[submodule "vendor/Net-HTTPServer"]
path = vendor/Net-HTTPServer
url = ssh://git/srv/git/vendor/Net-HTTPServer.git
[submodule "vendor/File-Grep"]
path = vendor/File-Grep
url = ssh://git/srv/git/vendor/File-Grep.git
[submodule "tigra"]
path = tigra
url = ssh://git//srv/git/tigra.git
[submodule "genome-music-testdata"]
path = genome-music-testdata
url = ssh://git//srv/git/genome-music-testdata.git
[submodule "varscan"]
path = varscan
url = ssh://git//srv/git/varscan.git
[submodule "tigra-sv"]
path = tigra-sv
url = ssh://git/srv/git/tigra-sv.git
[submodule "breakdancer"]
path = breakdancer
url = git://github.com/genome/breakdancer.git
[submodule "genome-db-cosmic"]
path = genome-db-cosmic
url = ssh://git//srv/git/genome-db-cosmic.git
[submodule "genome-db-omim"]
path = genome-db-omim
url = ssh://git//srv/git/genome-db-omim.git
[submodule "genome-db-pfam"]
path = genome-db-pfam
url = ssh://git//srv/git/genome-db-pfam.git
[submodule "bam-readcount"]
path = bam-readcount
url = ssh://git//srv/git/bam-readcount.git
[submodule "ur"]
path = ur
url = ssh://apipe-review.gsc.wustl.edu:29418/UR
[submodule "workflow"]
path = workflow
url = ssh://apipe-review.gsc.wustl.edu:29418/workflow
[submodule "jenkins"]
path = jenkins
url = https://github.com/genome/wugc-hudson.git
[submodule "getopt-complete"]
path = getopt-complete
url = https://github.com/genome/Getopt--Complete-for-Perl.git
[submodule "bassovac"]
path = bassovac
url = ssh://git/srv/git/bassovac.git
[submodule "graphite"]
path = graphite
url = https://github.com/genome/graphite.git
[submodule "fqgrep"]
path = fqgrep
url = https://github.com/genome/fqgrep.git
[submodule "sff2fastq"]
path = sff2fastq
url = https://github.com/genome/sff2fastq.git
[submodule "cron"]
path = cron
url = ssh://git/srv/git/genome_cron.git
[submodule "pairoscope"]
path = pairoscope
url = ssh://git//srv/git/pairoscope.git
[submodule "alignment_summary"]
path = alignment_summary
url = ssh://git//srv/git/alignment_summary.git
[submodule "vendor/tophat"]
path = vendor/tophat
url = git@github.com:genome-vendor/tophat.git
[submodule "vendor/libbio-samtools-perl"]
path = vendor/libbio-samtools-perl
url = ssh://git/srv/git/vendor/libbio-samtools-perl
[submodule "vendor/samtools"]
path = vendor/samtools
url = ssh://git/srv/git/vendor/samtools
[submodule "vendor/bwa"]
path = vendor/bwa
url = git://github.com/genome-vendor/bwa.git
[submodule "vendor/apollo"]
path = vendor/apollo
url = git@github.com:genome-vendor/apollo.git
[submodule "vendor/mutalin"]
path = vendor/mutalin
url = git@github.com:genome-vendor/mutalin.git
[submodule "vendor/cufflinks"]
path = vendor/cufflinks
url = git@github.com:genome-vendor/cufflinks.git
[submodule "vendor/velvet"]
path = vendor/velvet
url = git@github.com:genome-vendor/velvet.git
[submodule "vendor/samtools-hybrid"]
path = vendor/samtools-hybrid
url = git@github.com:genome-vendor/samtools-0.1.7a-hybrid.git
[submodule "vendor/bsmap"]
path = vendor/bsmap
url = git@github.com:genome-vendor/bsmap.git
[submodule "vendor/allpathslg"]
path = vendor/allpathslg
url = git@github.com:genome-vendor/allpathslg.git
[submodule "vendor/ensembl"]
path = vendor/ensembl
url = git@github.com:genome-vendor/ensembl.git
[submodule "vendor/CummeRbund"]
path = vendor/CummeRbund
url = git@github.com:genome-vendor/CummeRbund.git
[submodule "tgi-etc"]
path = tgi-etc
url = ssh://git/srv/git/genome-tgi-etc.git
[submodule "vendor/pindel"]
path = vendor/pindel
url = git@github.com:genome/pindel.git
[submodule "vendor/dendrix"]
path = vendor/dendrix
url = git@github.com:genome-vendor/Dendrix.git
[submodule "vendor/hotnet"]
path = vendor/hotnet
url = git@github.com:genome-vendor/HotNet.git
[submodule "vendor/File-lockf"]
path = vendor/File-lockf
url = http://github.com/genome-vendor/File-Lockf.git
[submodule "vendor/statgen"]
path = vendor/statgen
url = git@github.com:genome-vendor/statgen.git
[submodule "vendor/tophat-fusion"]
path = vendor/tophat-fusion
url = git@github.com:genome-vendor/tophat-fusion.git
[submodule "vendor/MGLtools"]
path = vendor/MGLtools
url = git@github.com:genome-vendor/MGLtools.git
[submodule "vendor/savant"]
path = vendor/savant
url = git://github.com/genome-vendor/savant.git
[submodule "vendor/freebayes"]
path = vendor/freebayes
url = git@github.com:genome-vendor/freebayes.git
[submodule "vendor/FLASH"]
path = vendor/FLASH
url = git@github.com:genome-vendor/FLASH.git
[submodule "vendor/chimerascan"]
path = vendor/chimerascan
url = git@github.com:genome-vendor/chimerascan.git
[submodule "vendor/r-cran-gplots"]
path = vendor/r-cran-gplots
url = git@github.com:genome-vendor/r-cran-gplots.git
[submodule "vendor/r-cran-bitops"]
path = vendor/r-cran-bitops
url = git@github.com:genome-vendor/r-cran-bitops.git
[submodule "vendor/r-cran-catools"]
path = vendor/r-cran-catools
url = git@github.com:genome-vendor/r-cran-catools.git
[submodule "vendor/r-cran-h5r"]
path = vendor/r-cran-h5r
url = git@github.com:genome-vendor/r-cran-h5r.git
[submodule "vendor/r-cran-pbh5"]
path = vendor/r-cran-pbh5
url = git@github.com:genome-vendor/r-cran-pbh5
[submodule "vendor/r-bioc-lumi"]
path = vendor/r-bioc-lumi
url = git@github.com:genome-vendor/r-bioc-lumi.git
[submodule "vendor/r-bioc-biobase"]
path = vendor/r-bioc-biobase
url = git@github.com:genome-vendor/r-bioc-biobase.git
[submodule "genome-snapshot-testdata"]
path = genome-snapshot-testdata
url = ssh://git//srv/git/genome-snapshot-testdata.git
[submodule "vendor/libstatistics-robust-scale-perl"]
path = vendor/libstatistics-robust-scale-perl
url = git@github.com:genome-vendor/libstatistics-robust-scale-perl.git
[submodule "vendor/r-cran-skat"]
path = vendor/r-cran-skat
url = git@github.com:genome-vendor/r-cran-skat.git
[submodule "vendor/bowtie"]
path = vendor/bowtie
url = git@github.com:genome-vendor/bowtie.git
[submodule "vendor/r-cran-ggplot2"]
path = vendor/r-cran-ggplot2
url = git@github.com:genome-vendor/r-cran-ggplot2.git
[submodule "vendor/MetaVelvet"]
path = vendor/MetaVelvet
url = git@github.com:genome-vendor/MetaVelvet.git
[submodule "vendor/Statistics-TTest"]
path = vendor/Statistics-TTest
url = git@github.com:genome-vendor/Statistics-TTest.git
[submodule "vendor/bedtools"]
path = vendor/bedtools
url = git@github.com:genome-vendor/bedtools.git
[submodule "genome-snapshot-deps"]
path = genome-snapshot-deps
url = ssh://git/srv/git/genome-snapshot-deps.git
[submodule "vendor/polymutt"]
path = vendor/polymutt
url = git@github.com:genome-vendor/polymutt.git
[submodule "vendor/trinity"]
path = vendor/trinity
url = git@github.com:genome-vendor/trinity.git
[submodule "vendor/r-cran-rcurl"]
path = vendor/r-cran-rcurl
url = git@github.com:genome-vendor/r-cran-rcurl.git
[submodule "vendor/r-cran-chemminer"]
path = vendor/r-cran-chemminer
url = git@github.com:genome-vendor/r-cran-chemminer.git
[submodule "vendor/far"]
path = vendor/far
url = git@github.com:genome-vendor/far.git
[submodule "vendor/r-cran-fastcluster"]
path = vendor/r-cran-fastcluster
url = git@github.com:genome-vendor/r-cran-fastcluster.git
[submodule "vendor/r-cran-plyr"]
path = vendor/r-cran-plyr
url = git@github.com:genome-vendor/r-cran-plyr.git
[submodule "vendor/r-cran-reshape"]
path = vendor/r-cran-reshape
url = git@github.com:genome-vendor/r-cran-reshape.git
[submodule "vendor/r-cran-reshape2"]
path = vendor/r-cran-reshape2
url = git@github.com:genome-vendor/r-cran-reshape2.git
[submodule "vendor/r-cran-rsqlite"]
path = vendor/r-cran-rsqlite
url = git@github.com:genome-vendor/r-cran-rsqlite.git
[submodule "vendor/r-cran-stringr"]
path = vendor/r-cran-stringr
url = git@github.com:genome-vendor/r-cran-stringr.git
[submodule "vendor/VEP_plugins"]
path = vendor/VEP_plugins
url = https://github.com/genome-vendor/VEP_plugins.git
[submodule "bam-window"]
path = bam-window
url = ssh://git//srv/git/bam-window.git
[submodule "vendor/strelka"]
path = vendor/strelka
url = git@github.com:genome-vendor/strelka.git
[submodule "copyCat"]
path = copyCat
url = ssh://git//srv/git/copyCat.git
[submodule "sciClone"]
path = sciClone
url = git@github.com:genome/sciclone.git
[submodule "vendor/htseq"]
path = vendor/htseq
url = git@github.com:genome-vendor/htseq.git
[submodule "vendor/rna-star"]
path = vendor/rna-star
url = git@github.com:sakoht/rna-star.git
[submodule "configuration-manager"]
path = configuration-manager
url = https://github.com/genome/configuration-manager.git
[submodule "gms-config"]
path = gms-config
url = ssh://git/srv/git/gms-config.git
[submodule "vendor/gatk-protected"]
path = vendor/gatk-protected
url = git@github.com:genome-vendor/gatk-protected.git
[submodule "vendor/picard-tools"]
path = vendor/picard-tools
url = https://github.com/genome-vendor/picard-tools.git
[submodule "bmm"]
path = bmm
url = https://github.com/genome/bmm.git
[submodule "vendor/libset-intervaltree-perl"]
path = vendor/libset-intervaltree-perl
url = https://github.com/genome-vendor/libset-intervaltree-perl.git
[submodule "vendor/r-cran-normt3"]
path = vendor/r-cran-normt3
url = https://github.com/sakoht/r-cran-normt3.git
[submodule "vendor/dindel"]
path = vendor/dindel
url = https://github.com/genome/dindel.git
[submodule "vendor/circos"]
path = vendor/circos
url = https://github.com/genome-vendor/circos.git