blob: cb85344a16a95fa502a7ac5049f9f5b77eab7493 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
# 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=3.0.10
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=('93cfa802938506866b9d565a18a31ac84fd26f2929636b23f1f8dd9f39cf977d'
'2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d')
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
}
|