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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-06-25 14:21:16 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-06-25 14:21:16 +0200 |
| commit | 44863d23a814e72b31f589ad412f35a024282766 (patch) | |
| tree | 9c26b58ba5142007119c0d948ba07b97cfe3c7f6 | |
| parent | sci-biology/salmon: drop calls to curl, fix libdir (diff) | |
| download | sci-44863d23a814e72b31f589ad412f35a024282766.tar.gz sci-44863d23a814e72b31f589ad412f35a024282766.tar.bz2 sci-44863d23a814e72b31f589ad412f35a024282766.zip | |
sci-biology/salmon: bring -9999 in sync with 0.10.2.ebuild
The -9999 won't work as the SRC_URI section is not respected,
hence is commented out.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
| -rw-r--r-- | sci-biology/salmon/files/salmon-9999-no-boost-static.patch | 18 | ||||
| -rw-r--r-- | sci-biology/salmon/salmon-9999.ebuild | 30 |
2 files changed, 10 insertions, 38 deletions
diff --git a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch deleted file mode 100644 index 1a9665251..000000000 --- a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- salmon-9999/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200 -+++ salmon-9999/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200 -@@ -213,15 +213,6 @@ - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --if(CONDA_BUILD) -- set (Boost_USE_STATIC_LIBS OFF) --else () -- set (Boost_USE_STATIC_LIBS ON) --endif(CONDA_BUILD) -- - set (Boost_USE_MULTITHREADED ON) - #set (Boost_USE_STATIC_RUNTIME OFF) - diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index b5e748fd2..221418960 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -8,14 +8,21 @@ inherit multilib cmake-utils git-r3 DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" HOMEPAGE="https://github.com/COMBINE-lab/salmon" EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git" -# SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${PN}-0.10.2_RapMap.zip" +#SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip +# https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz +# https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz +# https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz +# https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz +# https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" LICENSE="GPL-3" SLOT="0" IUSE="" -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch ) +PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch + "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch + "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch + "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch ) # budled copies of: # sci-biology/bwa-0.7.12.5 @@ -57,20 +64,3 @@ RDEPEND="${DEPEND}" # see the many curl executions: # salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null -# -src_configure(){ - local mycmakeargs=( - "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/boost/" - "-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/" - "-DTBB_INSTALL_DIR=${EPREFIX}/usr" - "-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr" - ) - # BUG: the configure step runs automatically curl download of 3rd-party stuff - # https://github.com/COMBINE-lab/salmon/issues/19 - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - rm -rf "${ED}"/usr/tests || die -} |