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commit: cb254becffa1b3891a42871345dfdf2977b134fa |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Fri Dec 2 21:45:13 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Fri Dec 2 21:45:13 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb254bec |
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|
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sci-biology/freebayes: note the many bundled deps we need to unbundle |
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|
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Package-Manager: portage-2.3.2 |
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|
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sci-biology/freebayes/freebayes-9999.ebuild | 64 +++++++++++++++++++++++++++++ |
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1 file changed, 64 insertions(+) |
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|
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diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild |
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index 02bfc0b..3a2b70b 100644 |
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--- a/sci-biology/freebayes/freebayes-9999.ebuild |
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+++ b/sci-biology/freebayes/freebayes-9999.ebuild |
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@@ -17,9 +17,73 @@ IUSE="" |
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|
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DEPEND="" |
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RDEPEND="${DEPEND} |
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+ sci-biology/htslib |
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sci-biology/bamtools |
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sci-biology/samtools" |
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|
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+# $ git clone --recursive git://github.com/ekg/freebayes.git |
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+# Cloning into 'freebayes'... |
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+# remote: Counting objects: 4942, done. |
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+# remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942 |
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+# Receiving objects: 100% (4942/4942), 5.93 MiB | 1.13 MiB/s, done. |
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+# Resolving deltas: 100% (3274/3274), done. |
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+# Submodule 'SeqLib' (https://github.com/walaj/SeqLib.git) registered for path 'SeqLib' |
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+# Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for path 'bamtools' |
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+# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' |
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+# Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered for path 'test/bash-tap' |
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+# Submodule 'test/test-simple-bash' (https://github.com/ingydotnet/test-simple-bash.git) registered for path 'test/test-simple-bash' |
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+# Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for path 'vcflib' |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/bamtools'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/intervaltree'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/bash-tap'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/test-simple-bash'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib'... |
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+# Submodule path 'SeqLib': checked out 'cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8' |
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+# Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 'SeqLib/bwa' |
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+# Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered for path 'SeqLib/fermi-lite' |
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+# Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 'SeqLib/htslib' |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/bwa'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/fermi-lite'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/htslib'... |
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+# Submodule path 'SeqLib/bwa': checked out 'fbd4dbc03904eccd71cdca8cac7aa48da749c19c' |
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+# Submodule path 'SeqLib/fermi-lite': checked out '5bc90f8d70e2b66184eccbd223a3be714c914365' |
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+# Submodule path 'SeqLib/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382' |
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+# Submodule path 'bamtools': checked out 'e77a43f5097ea7eee432ee765049c6b246d49baa' |
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+# Submodule path 'intervaltree': checked out 'dbb4c513d1ad3baac516fc1484c995daf9b42838' |
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+# Submodule path 'test/bash-tap': checked out 'c38fbfa401600cc81ccda66bfc0da3ea56288d03' |
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+# Submodule path 'test/test-simple-bash': checked out '124673ff204b01c8e96b7fc9f9b32ee35d898acc' |
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+# Submodule path 'vcflib': checked out '5e3ce04f758c6df16bc4d242b18a24d725d2e6e5' |
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+# Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'vcflib/fastahack' |
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+# Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'vcflib/filevercmp' |
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+# Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'vcflib/fsom' |
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+# Submodule 'googletest' (https://github.com/google/googletest.git) registered for path 'vcflib/googletest' |
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+# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'vcflib/intervaltree' |
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+# Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'vcflib/multichoose' |
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+# Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'vcflib/smithwaterman' |
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+# Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'vcflib/tabixpp' |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fastahack'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/filevercmp'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fsom'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/googletest'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/intervaltree'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/multichoose'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/smithwaterman'... |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp'... |
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+# Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' |
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+# Submodule path 'vcflib/filevercmp': checked out '1a9b779b93d0b244040274794d402106907b71b7' |
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+# Submodule path 'vcflib/fsom': checked out 'a6ef318fbd347c53189384aef7f670c0e6ce89a3' |
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+# Submodule path 'vcflib/googletest': checked out 'd225acc90bc3a8c420a9bcd1f033033c1ccd7fe0' |
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+# Submodule path 'vcflib/intervaltree': checked out 'b704f195e9b51d44dad68e33c209b06e63ebb353' |
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+# Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5' |
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+# Submodule path 'vcflib/smithwaterman': checked out '84c08d7eae7211d87fbcb1871dae20e6c2041e96' |
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+# Submodule path 'vcflib/tabixpp': checked out '80012f86dc22b13c75b73baf38195956db92473e' |
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+# Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'vcflib/tabixpp/htslib' |
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+# Cloning into '/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/tabixpp/htslib'... |
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+# Submodule path 'vcflib/tabixpp/htslib': checked out '0f298ce22c5c825c506129bf242348a31630c382' |
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+ |
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+# 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 |
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+ |
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src_install(){ |
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dobin bin/freebayes bin/bamleftalign |
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} |
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