commit: 3135d13c5e61485a195eeade8c0486176dd83264 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Mar 6 11:04:43 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Mar 6 11:04:43 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3135d13c
sci-biology/freebayes: version bump 1.3.5, EAPI bump fix build, use the meson build file Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/freebayes/freebayes-1.3.5.ebuild | 25 ++++++ sci-biology/freebayes/freebayes-9999.ebuild | 110 --------------------------- 2 files changed, 25 insertions(+), 110 deletions(-) diff --git a/sci-biology/freebayes/freebayes-1.3.5.ebuild b/sci-biology/freebayes/freebayes-1.3.5.ebuild new file mode 100644 index 000000000..836508195 --- /dev/null +++ b/sci-biology/freebayes/freebayes-1.3.5.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit meson + +DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms" +HOMEPAGE="https://github.com/ekg/freebayes"; +SRC_URI="https://github.com/freebayes/freebayes/releases/download/v${PV}/${P}-src.tar.gz"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +# tests not included in release tarball? +RESTRICT="test" + +DEPEND="" +RDEPEND="${DEPEND} + sci-libs/htslib + sci-biology/bamtools + sci-biology/samtools:*" + +S="${WORKDIR}/${PN}" diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild deleted file mode 100644 index 34b92b2ef..000000000 --- a/sci-biology/freebayes/freebayes-9999.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils git-r3 toolchain-funcs - -DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms" -HOMEPAGE="https://github.com/ekg/freebayes"; -EGIT_REPO_URI="https://github.com/ekg/freebayes.git"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -IUSE="" - -CDEPEND="dev-util/cmake" -DEPEND="" -RDEPEND="${DEPEND} - sci-libs/htslib - sci-biology/bamtools - sci-biology/samtools:*" - -# $ git clone --recursive https://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_prepare(){ - find . -name Makefile | while read f; do \ - sed -e "s/-O3 -D_FILE_OFFSET_BITS=64/${CFLAGS}/" -i $f || die - sed -e "s/^CFLAGS:= -O3/CFLAGS ?= ${CFLAGS}/" -i $f || die - sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/;s/^CXX=g++/CXX = $(tc-getCXX)/" -i $f || die - sed -e "s/g++ /$(tc-getCXX) /" -i $f || die - sed -e "s/-O3/${CXXFLAGS}/" -i $f || die - sed -e "s/^CC[ ]*=[ ]gcc/CC = $(tc-getCC)/" -i $f || die - sed -e "s/-g -Wall -O2/${CFLAGS}/;s/-g -Wall -Wno-unused-function -O2/${CFLAGS}/" -i $f || die - sed -e "s/-O3 /${CFLAGS}/;s/ -O3/${CFLAGS}/" -i $f || die - done - sed -e "s/^C=gcc/C = $(tc-getCC)/" -i Makefile || die - sed -e "s/gcc/$(tc-getCC)/" -i SeqLib/bwa/Makefile SeqLib/fermi-lite/Makefile || die - sed -e "s/g++/$(tc-getCXX)/" -i SeqLib/src/Makefile.am || die - default -} - -src_compile(){ - emake -j1 # vcflib/smithwaterman/ sometimes does not compile -} - -src_install(){ - dobin bin/freebayes bin/bamleftalign -}
