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# Maintainer: Bipin Kumar <bipin@ccmb.res.in>
# 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>
pkgname=sra-tools
_dep=ncbi-vdb
pkgver=3.0.2
_depver=3.0.2
pkgrel=2
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-$_depver.tar.gz::https://github.com/ncbi/ncbi-vdb/archive/refs/tags/$_depver.tar.gz")
license=('custom: Public Domain')
provides=('ncbi-vdb')
arch=(x86_64)
depends=('hdf5' 'python' 'mbedtls' 'libxml2')
makedepends=('cmake' 'doxygen' 'java-runtime' 'patchelf')
sha256sums=('44b87153f25366dc16cbb1a23b1db71dad9a5b9dac58c0692404120d8eede7c8'
'275ccb225ddb156688c8c71f772f73276cb18ebff773a51150f86f8002ed2d59')
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-$_depver"
install -d build1
cd build1
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=lib
make
cd ${srcdir}/"$pkgname-$pkgver"
install -d build1
cd build1
cmake .. -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=lib \
-DVDB_INCDIR="$srcdir/$_dep-$_depver/interfaces/" \
-DVDB_LIBDIR="$srcdir/$_dep-$_depver/build1/lib/" \
make
}
package(){
install -d $srcdir/$_dep-$_depver/interfaces/kfg/ncbi/etc/profile.d/
cd "$_dep-$_depver"/build1
make DESTDIR="$pkgdir" install
cd ${srcdir}/"$pkgname-$pkgver"/build1
make DESTDIR="$pkgdir" install
cp -rf ${srcdir}/"$pkgname-$pkgver"/etc "$pkgdir"
cp -rf $srcdir/$_dep-$_depver/interfaces/kfg/ncbi/etc "$pkgdir"
# install LICENSE file
install -Dm644 ${srcdir}/"$pkgname-$pkgver"/LICENSE -t "$pkgdir"/usr/share/licenses/sra-tools/
# remove empty folder
rm -Rf "$pkgdir"/usr/include/kfg/ncbi/etc/
# remove symlinks, fix Insecure Runpaths, and fix filenames
patchelf --remove-rpath "$pkgdir"/usr/lib/libncbi-ngs.so.3.0.2
find "$pkgdir"/usr/bin -type l -delete
for filename in "$pkgdir"/usr/bin/*
do [ -f "$filename" ] || continue
patchelf --remove-rpath $filename
mv "$filename" "${filename//.${pkgver}/}"
done
}
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