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# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=tophat
pkgver=2.1.2
pkgrel=3
pkgdesc="fast splice junction mapper for RNA-Seq reads"
arch=('x86_64' 'i686')
url="http://ccb.jhu.edu/software/tophat/index.shtml"
license=('custom')
depends=('boost-libs' 'bowtie2' 'python')
makedepends=('boost' 'clang')
source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DaehwanKimLab/tophat/archive/refs/tags/v${pkgver}.tar.gz"
'make_pair.patch'
'configure.patch'
)
md5sums=('db844fd7f53c519e716cd6222e6195b2'
'4f53cd3e611c2a0744babede14c3ae66'
'175420b0b08f2979d9585ec55cbeb0ee')
prepare() {
cd $srcdir/$pkgname-$pkgver
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-fusion-post \
# src/tophat.py
# to python3
2to3 -w -n .
patch -Np1 -i $srcdir/make_pair.patch
patch -Np0 -i $srcdir/configure.patch
autoreconf -i
autoupdate
autoconf
}
build() {
cd $srcdir/$pkgname-$pkgver
export CC=clang
export CXX=clang++
./configure --prefix=/usr --with-python-sys-prefix
# 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
# fix python install
_pyver=$(python -V | cut -d ' ' -f2)
install -d $pkgdir/usr/lib/python${_pyver:0:4}/site-packages
mv \
-t $pkgdir/usr/lib/python${_pyver:0:4}/site-packages \
$pkgdir/usr/bin/{intervaltree,sortedcontainers}
install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
}
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