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# Maintainer: zfo <zfoofz1@gmail.com>
# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
pkgname=seqan-git
_pkgname=seqan
pkgver=r.fcad60a
pkgrel=1
pkgdesc='C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data'
arch=('i686' 'x86_64')
url="http://www.seqan.de/"
license=('custom')
depends=('bash' 'bzip2' 'zlib')
makedepends=('cmake')
conflicts=('seqan' 'seqan2')
source=()
md5sums=()
_gitroot=https://github.com/seqan/seqan
_gitname=seqan
update_git(){
cd "$srcdir"
msg "Connecting to GIT server...."
if [[ -d "$_gitname" ]]; then
cd "$_gitname" && git pull origin >&2
msg "The local files are updated."
else
git clone --depth 1 "$_gitroot" "$_gitname" >&2
fi
msg "GIT checkout done or server timeout"
}
pkgver() {
update_git
cd "${srcdir}/${_gitname}"
printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
}
build() {
msg "Starting build..."
#zfo: this seems to me unnecessary
#rm -rf "$srcdir/$_gitname-build"
if [[ -d "$_gitname" ]]; then
cd "$srcdir/$_gitname-build" && git pull origin
else
git clone "$srcdir/$_gitname" "$srcdir/$_gitname-build"
fi
cd "$srcdir/$_gitname-build"
# common patching (aka prepare)
mkdir -p build
sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
-i $(grep -rl '/usr/bin/env python')
###
cd "$srcdir/$_gitname-build"/build
cmake \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_BUILD_TYPE=Release \
-DPYTHON_EXECUTABLE=/usr/bin/python2 \
-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE \
..
make
}
package() {
cd "$srcdir/$_gitname-build"/build
make prefix=/usr DESTDIR=$pkgdir install
install -Dm644 $pkgdir/usr/share/doc/sak/man/sak.1 $pkgdir/usr/share/man/man1/sak.1
rm $pkgdir/usr/share/doc/sak/man/sak.1
rmdir $pkgdir/usr/share/doc/sak/man
install -Dm644 ../LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
# install popular apps
files=("mason_frag_sequencing" "mason_genome" "mason_materializer" "mason_methylation"
"mason_simulator" "mason_splicing" "mason_tests" "mason_variator")
for file in "${files[@]}" ; do
install -m755 bin/$file $pkgdir/usr/bin/$file
done
}
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