diff options
-rw-r--r-- | PKGBUILD | 19 |
1 files changed, 13 insertions, 6 deletions
@@ -1,6 +1,6 @@ -# Maintainer: Thiago L. A. Miller <thiago_leisrael@hotmail.com> +# Maintainer: Saulius Lukauskas <luksaulius@gmail.com> pkgname=salmon -pkgver=0.13.1 +pkgver=1.3.0 pkgrel=1 pkgdesc="Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments" arch=('x86_64') @@ -10,22 +10,29 @@ 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=('bae03f0e2b30d976029f83e745a3ad65') +md5sums=('ec4fc93d95bbcc782d63578e8f2624fd') prepare() { - # Fix for now segmentation fault when using archlinux jemalloc package - # Force cmake to statically build jemalloc from salmon's dev sources cd "$pkgname-$pkgver" - sed -i '/^find_package(Jemalloc)/ , /^endif()/ s/^/#/' CMakeLists.txt + + # 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 } |