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-rw-r--r--PKGBUILD32
1 files changed, 21 insertions, 11 deletions
diff --git a/PKGBUILD b/PKGBUILD
index bcfa82544eab..41c5908e5f3a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,15 +1,15 @@
-# Maintainer: bipin kumar <bipin@ccmb.res.in>
+# Maintainer: bipin kumar <kbipinkumar@pm.me>
# Contributor: Saulius Lukauskas <luksaulius@gmail.com>
# Contributor: Thiago L. A. Miller <thiago_leisrael@hotmail.com>
pkgname=salmon
pkgver=1.10.1
-pkgrel=1
+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/$pkgname/"
-license=('GPL')
-depends=('intel-tbb' 'jemalloc' 'boost-libs' 'bzip2')
-makedepends=('boost>=1.55' 'cmake' 'unzip' 'cereal')
+license=('GPL3')
+depends=('intel-tbb' 'jemalloc' 'boost-libs')
+makedepends=('boost>=1.55' 'cmake' 'unzip' 'cereal' 'curl' 'bzip2')
options=('!emptydirs')
source=("$pkgname-$pkgver.tar.gz"::"https://github.com/COMBINE-lab/$pkgname/archive/v$pkgver.tar.gz")
sha256sums=('babd9ccc189cfea07566d8a11d047f25fad5b446b4b69257bc6ad8869f8b7707')
@@ -27,22 +27,32 @@ build() {
# FIXME: NO_IPO=TRUE is for some reason needed in 1.3.0
# Otherwise it is segfaulting...
- cmake \
+ cmake -B build \
-DNO_IPO:BOOL='TRUE' \
-DCMAKE_COLOR_MAKEFILE:BOOL='ON' \
-DCMAKE_INSTALL_PREFIX:PATH='/usr' \
+ -DCMAKE_SKIP_RPATH=YES \
-Wno-dev \
- -DUSE_SHARED_LIBS=ON \
- .
+ -DBOOST_INCLUDEDIR='/usr/include' \
+ -DBOOST_LIBRARYDIR='/usr/lib' \
+ -DUSE_SHARED_LIBS=ON
+
+ cmake --build build
+}
+
+check() {
+ cd "$pkgname-$pkgver"
+
+ ctest --test-dir build --output-on-failure
- make
}
package() {
cd "$pkgname-$pkgver"
- make DESTDIR="$pkgdir" install
+
+ DESTDIR="$pkgdir" cmake --install build
- install -Dm644 include/{*.h,*.hpp,*.tpp} -t ${pkgdir}/usr/include/${pkgname}
+ install -Dm644 include/{*.h,*.hpp,*.tpp} -t ${pkgdir}/usr/include/${pkgname}
# clear cmake files
rm -rf ${pkgdir}/usr/lib/{graphdump,ntcard,twopaco}