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# This is the PKGBUILD for ngs-python
# Maintainer: Georgios Amanakis <g_amanakis{at}yahoo{dt}com>
pkgname=ngs-python
_pkgname=ngs
pkgver=2.9.6
pkgrel=1
pkgdesc="A new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing."
arch=('x86_64')
url="https://github.com/ncbi/ngs"
depends=('java-environment' 'perl-file-copy-recursive' 'zlib' 'ncbi-vdb' 'ngs')
provides=('ngs-python')
license=('custom:PublicDomain')
source=("https://github.com/ncbi/ngs/archive/$pkgver.tar.gz" "ngs.patch" "ngs-python.patch")
md5sums=('d87f96dcfcaf4967ddbbf8de761641f8'
'3973d35d7a1b252eb6a426403a652ef9'
'105d75eb6e144af86569e1240e959702')
prepare(){
cd "${_pkgname}-${pkgver}"
# ncbi build process frequently checks if we are root user which interferes
# with makepkg use of fakeroot
patch -p1 -i $srcdir/ngs.patch
patch -p1 -i $srcdir/ngs-python.patch
}
build(){
cd "${_pkgname}-${pkgver}"
./configure --prefix="$pkgdir/usr/" --build-prefix="$srcdir/build"
cd ./ngs-python
./configure --prefix="$pkgdir/usr/" --build-prefix="$srcdir/build" --with-ngs-sdk-prefix="/usr" --with-ncbi-vdb-prefix="/usr"
cd ../
make -C ngs-sdk
make -C ngs-python
}
#check(){
# cd "${pkgname}-${pkgver}"
# make -k test
#}
package(){
cd "$_pkgname-$pkgver"
# ncbi does not use autoconf/automake so there is no respect for DESTDIR
# but there is a ROOT(dir)
#make "ROOT=$pkgdir" install
make -C ngs-python install
# add license
mkdir -p "$pkgdir/usr/share/licenses/${pkgname}"
cp "LICENSE" "$pkgdir/usr/share/licenses/${pkgname}/LICENSE"
}
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