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# This is the PKGBUILD for sra-tools
# Maintainer: Aaron Baker <aa{last name}99{at}gmail{dt}org>
# Maintainer: Georgios Amanakis <g_amanakis{at}yahoo{dt}com>
pkgname=sra-tools
pkgver=2.9.3
pkgrel=1
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="http://www.ncbi.nlm.nih.gov/Traces/sra/"
depends=('libxml2' 'file' 'hdf5' 'ngs' 'ncbi-vdb')
optdepends=('fuse: mount remote genome reference files')
provides=('sra-tools')
license=('custom:PublicDomain')
source=("$pkgname-$pkgver.tar.gz::https://github.com/ncbi/sra-tools/archive/$pkgver.tar.gz"
"sra-tools.patch")
sha256sums=('531c8ce774c9807df091005a23cdf88a63d6efb2be2e38342406af90e4db15c9'
'59c87371b10a3d8f7c1c8312c534ec9a6374cb3428ecbeb42c60cf422cab0782')
prepare(){
cd $pkgname-$pkgver
# sra-tools tries to link to hdf5 as a static library but Arch provides this as
# a dynamic library https://bbs.archlinux.org/viewtopic.php?id=208018
sed -e 's/-shdf5/-lhdf5/' -i tools/pacbio-load/Makefile
patch -p1 -i ../sra-tools.patch
}
build(){
cd "${pkgname}-${pkgver}"
./configure \
--prefix="$pkgdir/usr/" \
--build-prefix="$srcdir/build_dir" \
--with-ngs-sdk-prefix="/usr" \
--with-ncbi-vdb-sources="/usr/src/ncbi-vdb-$pkgver" \
--with-ncbi-vdb-build="/usr/src/ncbi-vdb-$pkgver/build_dir"
make
}
check(){
cd "${pkgname}-${pkgver}"
# make -k test
}
package(){
cd "$pkgname-$pkgver"
# make "ROOT=$pkgdir" install
make install
# add the license
mkdir -p "$pkgdir/usr/share/licenses/${pkgname}"
cp "LICENSE" "$pkgdir/usr/share/licenses/${pkgname}/LICENSE"
}
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