diff options
-rw-r--r-- | .SRCINFO | 39 | ||||
-rw-r--r-- | PKGBUILD | 87 |
2 files changed, 126 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..5c539907bea0 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,39 @@ +pkgbase = freebayes-git + pkgdesc = A tool for finding polymorphisms in high throughput sequence data. + pkgver = 1.0.1.r0.gefe685d + pkgrel = 1 + url = https://github.com/ekg/freebayes + arch = i686 + arch = x86_64 + license = MIT + makedepends = git + depends = gcc-libs + depends = zlib + provides = freebayes + source = git://github.com/ekg/freebayes.git + source = git://github.com/ekg/bamtools.git + source = git://github.com/ekg/intervaltree.git + source = git://github.com/illusori/bash-tap.git + source = git://github.com/ingydotnet/test-simple-bash.git + source = git://github.com/ekg/vcflib.git + source = git://github.com/ekg/fastahack.git + source = git://github.com/ekg/filevercmp.git + source = git://github.com/ekg/fsom.git + source = git://github.com/ekg/multichoose.git + source = git://github.com/ekg/smithwaterman.git + source = git://github.com/ekg/tabixpp.git + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + md5sums = SKIP + +pkgname = freebayes-git + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..4a5c50b50438 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,87 @@ +# Maintainer: Sedeer el-Showk <s.elshowk@netherrealm.net> + +pkgname=freebayes-git +pkgver=1.0.1.r0.gefe685d +pkgrel=1 +pkgdesc='A tool for finding polymorphisms in high throughput sequence data.' +arch=('i686' 'x86_64') +url="https://github.com/ekg/freebayes" +license=('MIT') +depends=('gcc-libs' 'zlib') +makedepends=('git') +provides=('freebayes') +source=('git://github.com/ekg/freebayes.git' + 'git://github.com/ekg/bamtools.git' + 'git://github.com/ekg/intervaltree.git' + 'git://github.com/illusori/bash-tap.git' + 'git://github.com/ingydotnet/test-simple-bash.git' + 'git://github.com/ekg/vcflib.git' + 'git://github.com/ekg/fastahack.git' + 'git://github.com/ekg/filevercmp.git' + 'git://github.com/ekg/fsom.git' + 'git://github.com/ekg/multichoose.git' + 'git://github.com/ekg/smithwaterman.git' + 'git://github.com/ekg/tabixpp.git') +md5sums=(SKIP SKIP SKIP SKIP SKIP SKIP SKIP SKIP SKIP SKIP SKIP SKIP) +MAKEFLAGS="-j1" # Multi-threaded build fails + +pkgver() { + cd $srcdir/${pkgname%-git} + git describe --long --tags | sed 's/^v//;s/\([^-]*-g\)/r\1/;s/-/./g' +} + +prepare() { + cp -a intervaltree intervaltree-vcflib + + cd ${pkgname%-git} + git submodule | sed -e 's/^[- ]//' > ../module-heads + cd .. + + for module in {bamtools,intervaltree,bash-tap,test-simple-bash,vcflib}; do + cd ${module} + git checkout `grep ${module} ../module-heads | cut -d" " -f1` + cd .. + done + + cd vcflib + git submodule | sed -e 's/^[- ]//' > ../vcflibmodule-heads + cd .. + + for module in {fastahack,filevercmp,fsom,intervaltree-vcflib,multichoose,smithwaterman,tabixpp}; do + cd ${module} + git checkout `grep ${module%-vcflib} ../vcflibmodule-heads | cut -d" " -f1` + cd .. + done + + cd ${pkgname%-git} + git submodule init + git config submodule.bamtools.url "$srcdir/bamtools" + git config submodule.intervaltree.url "$srcdir/intervaltree" + git config submodule.bash-tap.url "$srcdir/bash-tap" + git config submodule.test/test-simply-bash.url "$srcdir/test-simple-bash" + git config submodule.vcflib.url "$srcdir/vcflib" + git submodule update + + cd vcflib + git submodule init + git config submodule.fastahack.url "$srcdir/fastahack" + git config submodule.filevercmp.url "$srcdir/filevercmp" + git config submodule.fsom.url "$srcdir/fsom" + git config submodule.intervaltree.url "$srcdir/intervaltree-vcflib" + git config submodule.multichoose.url "$srcdir/multichoose" + git config submodule.smithwaterman.url "$srcdir/smithwaterman" + git config submodule.tabixpp.url "$srcdir/tabixpp" + git submodule update +} + +build() { + cd $srcdir/${pkgname%-git} + make +} + +package() { + install -Dm644 $srcdir/${pkgname%-git}/LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE + for f in {freebayes,bamleftalign}; do + install -D $srcdir/${pkgname%-git}/bin/$f $pkgdir/usr/bin/$f + done +} |