mirror of
https://github.com/BioArchLinux/Packages.git
synced 2025-03-10 12:02:42 +00:00
72 lines
2 KiB
Bash
72 lines
2 KiB
Bash
# Maintainer: bipin kumar <kbipinkumar@pm.me>
|
|
# Contributor: Saulius Lukauskas <luksaulius@gmail.com>
|
|
# Contributor: Thiago L. A. Miller <thiago_leisrael@hotmail.com>
|
|
pkgname=salmon
|
|
pkgver=1.10.3
|
|
pkgrel=3
|
|
pkgdesc="Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments"
|
|
arch=('x86_64')
|
|
url="https://combine-lab.github.io/$pkgname/"
|
|
license=('GPL3')
|
|
depends=('intel-tbb' 'bzip2' 'jemalloc' 'boost-libs' 'gcc-libs' 'xz' 'zlib' 'glibc')
|
|
makedepends=('boost>=1.55' 'cmake' 'unzip' 'cereal' 'curl' 'bzip2' 'python-sphinx')
|
|
options=('!emptydirs')
|
|
source=("$pkgname-$pkgver.tar.gz"::"https://github.com/COMBINE-lab/$pkgname/archive/v$pkgver.tar.gz")
|
|
sha256sums=('a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871')
|
|
|
|
prepare() {
|
|
cd "$pkgname-$pkgver"
|
|
|
|
# Add missing include <string> in 1.3.0 headers
|
|
sed -i 's/#include <unordered_map>/#include <unordered_map>\n#include <string>/g' include/BAMUtils.hpp
|
|
}
|
|
|
|
build() {
|
|
cd "$pkgname-$pkgver"
|
|
|
|
# FIXME: NO_IPO=TRUE is for some reason needed in 1.3.0
|
|
# Otherwise it is segfaulting...
|
|
|
|
cmake -B build \
|
|
-DNO_IPO:BOOL='TRUE' \
|
|
-DCMAKE_COLOR_MAKEFILE:BOOL='ON' \
|
|
-DCMAKE_INSTALL_PREFIX:PATH='/usr' \
|
|
-DCMAKE_SKIP_RPATH=YES \
|
|
-Wno-dev \
|
|
-DBOOST_INCLUDEDIR='/usr/include' \
|
|
-DBOOST_LIBRARYDIR='/usr/lib' \
|
|
-DUSE_SHARED_LIBS=ON
|
|
|
|
cmake --build build
|
|
# build manpages
|
|
cd doc
|
|
make man
|
|
}
|
|
|
|
check() {
|
|
cd "$pkgname-$pkgver"
|
|
|
|
ctest --test-dir build --output-on-failure
|
|
|
|
}
|
|
|
|
package() {
|
|
cd "$pkgname-$pkgver"
|
|
|
|
DESTDIR="$pkgdir" cmake --install build
|
|
|
|
install -Dm644 include/{*.h,*.hpp,*.tpp} -t ${pkgdir}/usr/include/${pkgname}
|
|
|
|
#install manpages
|
|
install -d ${pkgdir}/usr/share/man/man1/
|
|
install -Dm644 doc/build/man/salmon.1 ${pkgdir}/usr/share/man/man1/salmon.1
|
|
|
|
# clear cmake files
|
|
rm -rf ${pkgdir}/usr/lib/{graphdump,ntcard,twopaco}
|
|
}
|
|
|
|
# Local Variables:
|
|
# mode: shell-script
|
|
# sh-basic-offset: 2
|
|
# End:
|
|
# vim:set ts=2 sw=2 et:
|