From 4a1a638c80951e340e1a7175928e6ce7c46128d9 Mon Sep 17 00:00:00 2001 From: sukanka Date: Mon, 11 Jul 2022 18:56:07 +0800 Subject: [PATCH] freebayes: can be built now --- prepare/freebayes/PKGBUILD | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/prepare/freebayes/PKGBUILD b/prepare/freebayes/PKGBUILD index c380e9b9be..613d48035c 100644 --- a/prepare/freebayes/PKGBUILD +++ b/prepare/freebayes/PKGBUILD @@ -7,24 +7,23 @@ arch=('x86_64') url="https://github.com/freebayes/freebayes" license=('MIT') -depends=('tabixpp' 'vcflib' 'vcftools' 'samtools' 'parallel' 'bc') -makedepends=('ninja' 'meson' 'git' 'cmake' 'make') +depends=('tabixpp' 'htslib') +makedepends=('ninja' 'meson' 'git' 'cmake' 'make' +'vcflib' 'vcftools' 'samtools' 'parallel' 'bc') optdepends=() -source=(git+https://github.com/freebayes/freebayes.git#tag=v${pkgver}) +source=(git+https://github.com/freebayes/freebayes.git#tag=v${pkgver} +) noextract=() sha256sums=('SKIP') prepare() { cd "$pkgname" git submodule update --init --recursive - # find vcflib - sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" meson.build - sed -i "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" meson.build - # sed -i "167c include_directories : [ seqlib_inc]," meson.build # fix limits sed -i "/#include /d" intervaltree/IntervalTree.h sed -i "8i #include " intervaltree/IntervalTree.h + cp vcflib/tabixpp/tabix.* vcflib/src } build() { cd "$pkgname" @@ -35,6 +34,10 @@ build() { } package() { - cd "$pkgname-$pkgver" - install -Dm 755 build/freebayes $pkgdir/usr/bin/freebayes + cd "$pkgname" + install -Dm 755 build/freebayes -t $pkgdir/usr/bin/ + install -Dm 755 build/bamleftalign -t $pkgdir/usr/bin/ + cd build/libfreebayes_common.a.p + gcc -shared *.o -o libfreebayes_common.so + install -Dm755 libfreebayes_common.so -t $pkgdir/usr/lib/ }