Initial version

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
+}