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+# 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
+}