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# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
# Contributor: sukanka <su975853527 at gmail>
# Contributor: Aaron Baker <aa{last name}99{at}gmail{dt}org>
# Contributor: Georgios Amanakis <g_amanakis{at}yahoo{dt}com>
# Contributor: Guoyi Zhang <myname at malacology dot net>
pkgname=sra-tools
_dep=ncbi-vdb
pkgver=3.1.1
pkgrel=1
pkgdesc='A collection of tools and libraries for using data in the INSDC Sequence Read Archives'
url="https://github.com/ncbi/sra-tools"
source=("$pkgname-$pkgver.tar.gz::https://github.com/ncbi/sra-tools/archive/refs/tags/$pkgver.tar.gz"
"$_dep-$pkgver.tar.gz::https://github.com/ncbi/ncbi-vdb/archive/refs/tags/$pkgver.tar.gz")
license=('custom: Public Domain')
provides=('ncbi-vdb')
arch=(x86_64)
depends=('python' 'glibc' 'gcc-libs')
optdepends=('python-ngs: python module for ncbi sra-tools')
makedepends=('cmake' 'doxygen' 'java-runtime' 'hdf5' 'mbedtls' 'libxml2')
sha256sums=('96b110bd5a30ad312e2f02552062b48a77d40c763e6aba5bb84e83662a505cf1'
'e9766f259853c696be48e289b08cb5ae6e198d82d7ffee79f09ce7f720487991')
prepare(){
cd ${srcdir}/"$pkgname-$pkgver"
# fix permission denied in make install,
# and we manually install them.
sed -i 's|/etc/ncbi|${CMAKE_CURRENT_SOURCE_DIR}/etc/ncbi|g' build/env.cmake
sed -i 's|/etc/profile.d/sra-tools|${SRC_DIR}/etc/profile.d/sra-tools|g' build/install.sh
}
build(){
cd "$_dep-$pkgver"
install -d build1
cd build1
cmake .. -DCMAKE_BUILD_TYPE='None' \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_INSTALL_LIBDIR=lib \
-Wno-dev \
-DCMAKE_SKIP_RPATH=YES
make
cd ${srcdir}/"$pkgname-$pkgver"
install -d build1
cd build1
cmake .. -DCMAKE_BUILD_TYPE='None' \
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=lib \
-DVDB_INCDIR="$srcdir/$_dep-$pkgver/interfaces/" \
-DVDB_LIBDIR="$srcdir/$_dep-$pkgver/build1/lib/" \
-Wno-dev \
-DCMAKE_SKIP_RPATH=YES
make
}
package(){
install -d $srcdir/$_dep-$pkgver/interfaces/kfg/ncbi/etc/profile.d/
cd "$_dep-$pkgver"/build1
make DESTDIR="$pkgdir" install
cd ${srcdir}/"$pkgname-$pkgver"/build1
make DESTDIR="$pkgdir" install
cp -rf ${srcdir}/"$pkgname-$pkgver"/etc "$pkgdir"
cp -rf $srcdir/$_dep-$pkgver/interfaces/kfg/ncbi/etc "$pkgdir"
# install LICENSE file
install -Dm644 ${srcdir}/"$pkgname-$pkgver"/LICENSE -t "$pkgdir"/usr/share/licenses/sra-tools/
# remove empty folder
rm -Rf "$pkgdir"/usr/include/kfg/ncbi/etc/
# remove symlinks
find "$pkgdir"/usr/bin -type l -delete
# Fix filenames: remove $pkgever suffix from end of binaries
for bin in "$pkgdir"/usr/bin/*
do [ -f "$bin" ] || continue
mv --update=none "$bin" "${bin//.${pkgver}/}"
done
# Fix filenames: remove -orig suffix from end of binaries
for file in "$pkgdir"/usr/bin/*-orig; do mv --update=none "$file" "${file%-orig}"; done
}
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