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# This is the PKGBUILD for ncbi-vdb
# Maintainer: Aaron Baker <aa{last name}99{at}gmail{dt}org>
# Maintainer: Georgios Amanakis <g_amanakis{at}yahoo{dt}com>
pkgname=ncbi-vdb
pkgver=2.10.0
pkgrel=2
pkgdesc="The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."
arch=('x86_64')
url="https://github.com/ncbi/ncbi-vdb"
depends=('libxml2' 'ngs' 'hdf5')
provides=('ncbi-vdb')
license=('custom:PublicDomain')
options=('!strip' 'staticlibs')
source=("https://github.com/ncbi/ncbi-vdb/archive/$pkgver.tar.gz" "$pkgname.patch")
sha256sums=('a6cc88e8d12f536dc96d5f60698d0ef4cf2f63e31d3d12d23da39b1de39563e1'
'62550416a3bd48ad8d8810a4fde593f1e6fdc6b091afbcf903842f8a43da9f58')
prepare(){
cd "${pkgname}-${pkgver}"
# ncbi build process frequently checks if we are root user which interferes
# with makepkg use of fakeroot
patch -p1 -i $srcdir/$pkgname.patch
}
build(){
cd "${pkgname}-${pkgver}"
./configure --prefix="$pkgdir/usr/" \
--build-prefix="$srcdir/build_dir" \
--with-ngs-sdk-prefix="/usr" \
--with-ngs-java-prefix=/usr/share/java/ngs/ngs-java.jar
make
}
#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=$pkgdir" install
make install
mv "$pkgdir/usr/lib64" "$pkgdir/usr/lib"
# the source of this package is required by others
# TODO is there somewhere to put this for namcap not to complain?
mkdir -p "$pkgdir/usr/src/${pkgname}-${pkgver}/build_dir"
cp -r . "$pkgdir/usr/src/${pkgname}-${pkgver}"
cp -a "$srcdir/build_dir" "$pkgdir/usr/src/${pkgname}-${pkgver}"
# add the license
mkdir -p "$pkgdir/usr/share/licenses/${pkgname}"
cp "LICENSE" "$pkgdir/usr/share/licenses/${pkgname}/LICENSE"
# TODO without this a link from libncbi-vdb-static.a -> libncbi-vdb.a is dead because
# libncbi-vdb.a gets removed somehow??
# cd "$pkgdir/usr/lib/"
# ln -sf "libncbi-vdb.a.$pkgver" libncbi-vdb-static.a
# ln -sf "libncbi-wvdb.a.$pkgver" libncbi-wvdb-static.a
}
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