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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-12-02 22:45:13 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-12-02 22:45:13 +0100 |
| commit | cb254becffa1b3891a42871345dfdf2977b134fa (patch) | |
| tree | 860de3d4aac83bb230df3500abdcb5a1a382bb0b | |
| parent | sci-biology/ensembl-tools: note dependency not yet in science overlay (diff) | |
| download | sci-cb254bec.tar.gz sci-cb254bec.tar.bz2 sci-cb254bec.zip | |
sci-biology/freebayes: note the many bundled deps we need to unbundle
Package-Manager: portage-2.3.2
| -rw-r--r-- | sci-biology/freebayes/freebayes-9999.ebuild | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild index 02bfc0b39..3a2b70b4b 100644 --- a/sci-biology/freebayes/freebayes-9999.ebuild +++ b/sci-biology/freebayes/freebayes-9999.ebuild @@ -17,9 +17,73 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} + sci-biology/htslib sci-biology/bamtools sci-biology/samtools" +# $ git clone --recursive git://github.com/ekg/freebayes.git +# Cloning into 'freebayes'... +# remote: Counting objects: 4942, done. +# remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942 +# Receiving objects: 100% (4942/4942), 5.93 MiB | 1.13 MiB/s, done. +# Resolving deltas: 100% (3274/3274), done. +# Submodule 'SeqLib' (https://github.com/walaj/SeqLib.git) registered for path 'SeqLib' +# Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for path 'bamtools' +# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' +# Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'test/bash-tap' +# Submodule 'test/test-simple-bash' (https://github.com/ingydotnet/test-simple-bash.git) registered for path 'test/test-simple-bash' +# Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for path 'vcflib' +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/bamtools'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/intervaltree'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/bash-tap'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/test-simple-bash'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib'... +# Submodule path 'SeqLib': checked out 'cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8' +# Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 'SeqLib/bwa' +# Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered for path 'SeqLib/fermi-lite' +# Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 'SeqLib/htslib' +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/bwa'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/fermi-lite'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/htslib'... +# Submodule path 'SeqLib/bwa': checked out 'fbd4dbc03904eccd71cdca8cac7aa48da749c19c' +# Submodule path 'SeqLib/fermi-lite': checked out '5bc90f8d70e2b66184eccbd223a3be714c914365' +# Submodule path 'SeqLib/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382' +# Submodule path 'bamtools': checked out 'e77a43f5097ea7eee432ee765049c6b246d49baa' +# Submodule path 'intervaltree': checked out 'dbb4c513d1ad3baac516fc1484c995daf9b42838' +# Submodule path 'test/bash-tap': checked out 'c38fbfa401600cc81ccda66bfc0da3ea56288d03' +# Submodule path 'test/test-simple-bash': checked out '124673ff204b01c8e96b7fc9f9b32ee35d898acc' +# Submodule path 'vcflib': checked out '5e3ce04f758c6df16bc4d242b18a24d725d2e6e5' +# Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'vcflib/fastahack' +# Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'vcflib/filevercmp' +# Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'vcflib/fsom' +# Submodule 'googletest' (https://github.com/google/googletest.git) registered for path 'vcflib/googletest' +# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'vcflib/intervaltree' +# Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'vcflib/multichoose' +# Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'vcflib/smithwaterman' +# Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'vcflib/tabixpp' +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fastahack'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/filevercmp'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fsom'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/googletest'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/intervaltree'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/multichoose'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/smithwaterman'... +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp'... +# Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' +# Submodule path 'vcflib/filevercmp': checked out '1a9b779b93d0b244040274794d402106907b71b7' +# Submodule path 'vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3' +# Submodule path 'vcflib/googletest': checked out 'd225acc90bc3a8c420a9bcd1f033033c1ccd7fe0' +# Submodule path 'vcflib/intervaltree': checked out 'b704f195e9b51d44dad68e33c209b06e63ebb353' +# Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5' +# Submodule path 'vcflib/smithwaterman': checked out '84c08d7eae7211d87fbcb1871dae20e6c2041e96' +# Submodule path 'vcflib/tabixpp': checked out '80012f86dc22b13c75b73baf38195956db92473e' +# Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'vcflib/tabixpp/htslib' +# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp/htslib'... +# Submodule path 'vcflib/tabixpp/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382' + +# g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ -I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib -I../SeqLib -I../SeqLib/htslib -c freebayes.cpp + src_install(){ dobin bin/freebayes bin/bamleftalign } |