diff --git a/BioArchLinux/salmon/PKGBUILD b/BioArchLinux/salmon/PKGBUILD new file mode 100644 index 0000000000..591e764bce --- /dev/null +++ b/BioArchLinux/salmon/PKGBUILD @@ -0,0 +1,53 @@ +# Maintainer: bipin kumar +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/$pkgname/" +license=('GPL') +depends=('intel-tbb' 'jemalloc' 'boost-libs' 'bzip2') +makedepends=('boost>=1.55' 'cmake' 'unzip' 'cereal') +options=('!emptydirs') +source=("$pkgname-$pkgver.tar.gz"::"https://github.com/COMBINE-lab/$pkgname/archive/v$pkgver.tar.gz") +sha256sums=('450d953a5c43fe63fd745733f478d3fbaf24d926cb52731fd38ee21c4990d613') + +prepare() { + cd "$pkgname-$pkgver" + + # Add missing include in 1.3.0 headers + sed -i 's/#include /#include \n#include /g' include/BAMUtils.hpp +} + +build() { + cd "$pkgname-$pkgver" + + # FIXME: NO_IPO=TRUE is for some reason needed in 1.3.0 + # Otherwise it is segfaulting... + + cmake \ + -DNO_IPO:BOOL='TRUE' \ + -DCMAKE_COLOR_MAKEFILE:BOOL='ON' \ + -DCMAKE_INSTALL_PREFIX:PATH='/usr' \ + -Wno-dev \ + -DUSE_SHARED_LIBS=ON \ + . + + make +} + +package() { + cd "$pkgname-$pkgver" + make DESTDIR="$pkgdir" install + + install -Dm644 include/{*.h,*.hpp,*.tpp} -t ${pkgdir}/usr/include/${pkgname} + + # 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: diff --git a/BioArchLinux/salmon/lilac.yaml b/BioArchLinux/salmon/lilac.yaml new file mode 100644 index 0000000000..bb31cf22f6 --- /dev/null +++ b/BioArchLinux/salmon/lilac.yaml @@ -0,0 +1,20 @@ +build_prefix: extra-x86_64 +maintainers: +- github: sukanka + email: su975853527@gmail.com + +pre_build_script: | + update_pkgver_and_pkgrel(_G.newver) + +post_build_script: | + git_pkgbuild_commit() + update_aur_repo() + +update_on: + - source: github + github: COMBINE-lab/salmon + use_latest_release: true + prefix: v + - source: aur + aur: salmon + - alias: boost-libs