diff options
| -rw-r--r-- | .AURINFO | 19 | ||||
| -rw-r--r-- | .SRCINFO | 19 | ||||
| -rw-r--r-- | PKGBUILD | 36 | ||||
| -rw-r--r-- | configure-rpath.patch | 34 |
4 files changed, 108 insertions, 0 deletions
diff --git a/.AURINFO b/.AURINFO new file mode 100644 index 000000000000..43603e276612 --- /dev/null +++ b/.AURINFO @@ -0,0 +1,19 @@ +pkgbase = sga + pkgdesc = de novo sequence assembler using string graphs + pkgver = 0.10.13 + pkgrel = 1 + url = https://github.com/jts/sga + arch = x86_64 + arch = i686 + license = GPL3 + makedepends = sparsehash + depends = bamtools + depends = jemalloc + depends = python + source = sga-0.10.13.tar.gz::https://github.com/jts/sga/archive/v0.10.13.tar.gz + source = configure-rpath.patch + md5sums = d4f6aefc48c940dba96cc6513649ecdd + md5sums = SKIP + +pkgname = sga + diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..43603e276612 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,19 @@ +pkgbase = sga + pkgdesc = de novo sequence assembler using string graphs + pkgver = 0.10.13 + pkgrel = 1 + url = https://github.com/jts/sga + arch = x86_64 + arch = i686 + license = GPL3 + makedepends = sparsehash + depends = bamtools + depends = jemalloc + depends = python + source = sga-0.10.13.tar.gz::https://github.com/jts/sga/archive/v0.10.13.tar.gz + source = configure-rpath.patch + md5sums = d4f6aefc48c940dba96cc6513649ecdd + md5sums = SKIP + +pkgname = sga + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..f879c950fecc --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,36 @@ +# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> + +pkgname=sga +pkgver=0.10.13 +pkgrel=1 +pkgdesc="de novo sequence assembler using string graphs" +arch=('x86_64' 'i686') +url="https://github.com/jts/sga" +license=('GPL3') +depends=('bamtools' 'jemalloc' 'python') +makedepends=('sparsehash') +source=("$pkgname-$pkgver.tar.gz::https://github.com/jts/sga/archive/v$pkgver.tar.gz" + 'configure-rpath.patch') +md5sums=('d4f6aefc48c940dba96cc6513649ecdd' + 'SKIP') + +prepare() { + cd $srcdir/$pkgname-$pkgver/src + + patch -p0 -i $srcdir/configure-rpath.patch +} + +build() { + cd $srcdir/$pkgname-$pkgver/src + + ./autogen.sh + ./configure --prefix=/usr --with-bamtools=/usr --with-jemalloc=/usr + + make +} + +package() { + cd $srcdir/$pkgname-$pkgver/src + + make DESTDIR=$pkgdir install +} diff --git a/configure-rpath.patch b/configure-rpath.patch new file mode 100644 index 000000000000..2ec981c5fb14 --- /dev/null +++ b/configure-rpath.patch @@ -0,0 +1,34 @@ +--- configure.ac 2014-01-17 21:16:36.000000000 +0100 ++++ /tmp/configure.ac.patched 2014-11-07 14:04:25.882803929 +0100 +@@ -32,8 +32,8 @@ + [specify directory containing the bamtools library (http://github.com/pezmaster31/bamtools)])) + + if test "$with_bamtools" -a -d "$with_bamtools"; then +- bamtools_ldflags="-Wl,-rpath,$with_bamtools/lib -L$with_bamtools/lib -Wl,-rpath,$with_bamtools/lib/bamtools -L$with_bamtools/lib/bamtools" +- bamtools_include="-I$with_bamtools/include -I$with_bamtools/include/bamtools" ++ bamtools_ldflags="" ++ bamtools_include="-I$with_bamtools/include/bamtools" + fi + + # Support for tcmalloc/jemalloc/hoard +@@ -52,17 +52,17 @@ + + # Set library path to user-selected allocator + if test "$with_hoard" -a -d "$with_hoard"; then +- external_malloc_ldflags="-Wl,-rpath,$with_hoard -L$with_hoard" ++ external_malloc_ldflags="" + enable_hoard=1 + fi + + if test "$with_tcmalloc" -a -d "$with_tcmalloc"; then +- external_malloc_ldflags="-Wl,-rpath,$with_tcmalloc -L$with_tcmalloc" ++ external_malloc_ldflags="" + enable_tcmalloc=1 + fi + + if test "$with_jemalloc" -a -d "$with_jemalloc"; then +- external_malloc_ldflags="-Wl,-rpath,$with_jemalloc -L$with_jemalloc" ++ external_malloc_ldflags="" + enable_jemalloc=1 + fi + |