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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>
pkgname=sra-tools
_dep=ncbi-vdb
pkgver=3.0.5
_depver=3.0.5
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' 'glibc' 'gcc-libs')
optdepends=('python-ngs')
makedepends=('cmake' 'doxygen' 'java-runtime')
sha256sums=('6dca9889ca9cfa83e9ce1c39bf7ae5654576fc79c4f608e902272a49573a05e0'
'a32672d7f76507a77ceb29f023855eaf5bf4d150ddd21b55c013b499f3b83735')
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='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/$_dep-$_depver/interfaces/" \
-DVDB_LIBDIR="$srcdir/$_dep-$_depver/build1/lib/" \
-Wno-dev \
-DCMAKE_SKIP_RPATH=YES
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 "$pkgdir"/usr/include/kfg/ncbi/etc/
# remove symlinks
find "$pkgdir"/usr/bin -type l -delete
# Fix filenames: remove $pkgever suffix from end of binaries
for bin in "$pkgdir"/usr/bin/*
do [ -f "$bin" ] || continue
mv -n "$bin" "${bin//.${pkgver}/}"
done
# Fix filenames: remove -orig suffix from end of binaries
for file in "$pkgdir"/usr/bin/*-orig; do mv "$file" "${file%-orig}"; done
}
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