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.gitmodules
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[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 = https://github.com/genome/UR.git
[submodule "workflow"]
path = workflow
url = https://github.com/genome/tgi-workflow.git
[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 = git@github.com:genome/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
[submodule "verifyBamId"]
path = vendor/verifyBamId
url = https://github.com/genome-vendor/verifyBamId.git
[submodule "vendor/bamUtil"]
path = vendor/bamUtil
url = https://github.com/genome-vendor/bamUtil.git
[submodule "vendor/star"]
path = vendor/star
url = git@github.com:genome-vendor/star.git
[submodule "sqitch/genome"]
path = sqitch/genome
url = https://github.com/genome/genome-sqitch.git