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| -rw-r--r-- | .SRCINFO | 18 | ||||
| -rw-r--r-- | PKGBUILD | 56 |
2 files changed, 74 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..90bec5940daf --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,18 @@ +pkgbase = tophat + pkgdesc = fast splice junction mapper for RNA-Seq reads + pkgver = 2.0.14 + pkgrel = 1 + url = http://ccb.jhu.edu/software/tophat/index.shtml + arch = x86_64 + arch = i686 + license = PerlArtistic + makedepends = boost + makedepends = clang + depends = boost-libs + depends = bowtie2 + depends = python2 + source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz + md5sums = 509f72082c98f116131e976681578a9f + +pkgname = tophat + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..92cd0937ed38 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,56 @@ +# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> + +pkgname=tophat +pkgver=2.0.14 +pkgrel=1 +pkgdesc="fast splice junction mapper for RNA-Seq reads" +arch=('x86_64' 'i686') +url="http://ccb.jhu.edu/software/tophat/index.shtml" +license=('PerlArtistic') +depends=('boost-libs' 'bowtie2' 'python2') +makedepends=('boost' 'clang') +source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz") +md5sums=('509f72082c98f116131e976681578a9f') + +prepare() { + cd $srcdir/$pkgname-$pkgver + + sed -e 's|-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized||' \ + -e '/define.*esyscmd/d' \ + -e 's/svnversion/Unversioned directory/' \ + -i configure.ac + + sed -e 's|make $(SAMPROG)|make -e $(SAMPROG)|' \ + -i src/Makefile.am + + sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ + -i src/bed_to_juncs \ + src/contig_to_chr_coords \ + src/sra_to_solid \ + src/tophat.py \ + src/tophat-fusion-post + + autoreconf -fi +} + +build() { + cd $srcdir/$pkgname-$pkgver + + export CC=clang + export CXX=clang++ + export PYTHON=python2 + + ./configure --prefix=/usr + + # do not link against system-installed libbam.a + sed -e 's|-L/usr/lib||' \ + -i Makefile src/Makefile + + make -j1 +} + +package() { + cd $srcdir/$pkgname-$pkgver + + make DESTDIR=$pkgdir install +} |