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# Maintainer: bipin kumar <bipin@ccmb.res.in>
pkgname=salmon
pkgver=1.9.0
pkgrel=1
pkgdesc="Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments"
arch=('x86_64')
url="https://combine-lab.github.io/$pkgname/"
license=('GPL')
depends=('bzip2' 'intel-tbb' 'xz')
makedepends=('boost>=1.55' 'cmake' 'unzip')
options=('!emptydirs')
source=("$pkgname-$pkgver.tar.gz"::"https://github.com/COMBINE-lab/$pkgname/archive/v$pkgver.tar.gz")
md5sums=('8bdb73fbda5209953d6c480a67f52a9f')
prepare() {
cd "$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-$pkgver"
# FIXME: NO_IPO=TRUE is for some reason needed in 1.3.0
# Otherwise it is segfaulting...
cmake \
-DNO_IPO:BOOL='TRUE' \
-DCMAKE_COLOR_MAKEFILE:BOOL='ON' \
-DCMAKE_INSTALL_PREFIX:PATH='/usr' \
-Wno-dev \
.
make
}
package() {
cd "$pkgname-$pkgver"
make DESTDIR="$pkgdir" install
}
# Local Variables:
# mode: shell-script
# sh-basic-offset: 2
# End:
# vim:set ts=2 sw=2 et:
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