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| author |   Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-03-22 14:46:22 +0100 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-03-22 14:46:22 +0100 |
| commit | 459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2 (patch) | |
| tree | 4e38c8baf07683c4d0885f9965c5fec877d857f2 /sci-biology | |
| parent | dev-java/*: clean up (diff) | |
| download | sci-459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2.tar.gz sci-459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2.tar.bz2 sci-459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2.zip | |
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@riseup.net>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/salmon/salmon-0.10.2.ebuild | 16 |
1 files changed, 15 insertions, 1 deletions
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 +} |