commit: 459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Mar 22 13:46:22 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Mar 22 13:46:22 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=459e5c72
sci-biology/salmon: fix library path https://github.com/gentoo/sci/issues/1058 Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/salmon/salmon-0.10.2.ebuild | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild index 914ab0e69..671309ed0 100644 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ b/sci-biology/salmon/salmon-0.10.2.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit cmake +inherit cmake multilib DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" HOMEPAGE="https://github.com/COMBINE-lab/salmon"; @@ -49,6 +49,8 @@ DEPEND=" app-arch/bzip2 app-arch/xz-utils dev-libs/boost:0[threads] + dev-libs/libdivsufsort + sci-biology/bwa >=dev-libs/jemalloc-5.0.1 >=dev-cpp/tbb-2018.20180312 " @@ -57,3 +59,15 @@ BDEPEND=" net-misc/curl app-arch/unzip " + +src_prepare() { + # use system libs + sed -i \ + -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \ + -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \ + -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \ + -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \ + src/CMakeLists.txt || die + + cmake_src_prepare +}
