commit: ed55a4e91d91312772ee71645ae280fba57ce4dc Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Jun 25 10:01:47 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Jun 25 10:01:47 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed55a4e9
sci-biology/salmon: drop deps on static boost, some ebuild cleanup Document zillions of cryptic dependencies of a lousy package https://github.com/Kingsford-Group/libgff/issues/1 https://github.com/COMBINE-lab/salmon/issues/236 https://github.com/COMBINE-lab/salmon/issues/19 Incomplete install docs are deemed to be at: http://salmon.readthedocs.io/en/latest/building.html#requirements-for-building-from-source Try the command below to see yourself: salmon-0.10.2 $ find . -type f | xargs grep curl 2>/dev/null Thanks to @kiwifb for comments at https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d Package-Manager: Portage-2.3.40, Repoman-2.3.9 .../files/salmon-0.10.2-no-boost-static.patch | 18 +++++++++++++++ .../files/salmon-0.10.2_remove_curl_call.patch | 12 ++++++++++ .../files/salmon-0.3.2-no-boost-static.patch | 20 ---------------- .../salmon/files/salmon-9999-no-boost-static.patch | 18 +++++++++++++++ sci-biology/salmon/salmon-0.10.2.ebuild | 26 ++++++++++++++++++--- sci-biology/salmon/salmon-0.3.2.ebuild | 27 ---------------------- sci-biology/salmon/salmon-0.4.2.ebuild | 27 ---------------------- sci-biology/salmon/salmon-0.5.0.ebuild | 27 ---------------------- sci-biology/salmon/salmon-0.9.1.ebuild | 25 -------------------- sci-biology/salmon/salmon-9999.ebuild | 24 +++++++++++++++++-- 10 files changed, 93 insertions(+), 131 deletions(-) diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch new file mode 100644 index 000000000..ac561d793 --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch @@ -0,0 +1,18 @@ +--- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200 ++++ salmon-0.10.2/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/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch new file mode 100644 index 000000000..8eddc6e3a --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch @@ -0,0 +1,12 @@ +--- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200 ++++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200 +@@ -29,7 +29,8 @@ + EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688 + + mkdir -p ${EXTERNAL_DIR} +-curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip ++# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip ++cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip + + hashcheck="" + if exists sha256sum; then diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch deleted file mode 100644 index 7ac3d0882..000000000 --- a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch +++ /dev/null @@ -1,20 +0,0 @@ -Do not force static and multithreaded boost libs, use what is available - -Patch by Michael Schubert - ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH ) - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --set (Boost_USE_STATIC_LIBS ON) --set (Boost_USE_MULTITHREADED ON) --#set (Boost_USE_STATIC_RUNTIME OFF) -- - find_package (ZLIB) - if (NOT ZLIB_FOUND) - message (FATAL_ERROR "zlib must be installed before configuration & building can proceed") diff --git a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch new file mode 100644 index 000000000..1a9665251 --- /dev/null +++ b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch @@ -0,0 +1,18 @@ +--- 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 ${CMAKE_LIBRARY_PATH}) + endif ( DEFINED CUSTOM_BOOST_PATH ) + +-## +-# We want static, multithreaded boost libraries +-## +-if(CONDA_BUILD) +- set (Boost_USE_STATIC_LIBS OFF) +-else () +- set (Boost_USE_STATIC_LIBS ON) +-endif(CONDA_BUILD) +- + set (Boost_USE_MULTITHREADED ON) + #set (Boost_USE_STATIC_RUNTIME OFF) + diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild index f97a32f18..540225019 100644 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ b/sci-biology/salmon/salmon-0.10.2.ebuild @@ -7,15 +7,35 @@ inherit cmake-utils DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc +PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch + "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch ) + +RDEPEND="${DEPEND}" +# budled copies of: +# sci-biology/bwa-0.7.12.5 +# sci-biology/jellyfish +# sci-biology/staden-1.14.8.1 +# sci-biology/gfftools +# +# libgff-1.1 from https://github.com/Kingsford-Group/libgff +# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz +# https://github.com/Kingsford-Group/libgff/issues/1 +# +# dev-libs/spdlog-0.16.1 +# cereal-1.2.2 +DEPEND="sys-libs/zlib + app-arch/bzip2 + app-arch/xz-utils + dev-libs/boost:0[threads] + >=dev-libs/jemalloc-5.0.1 >=dev-cpp/tbb-2018.20180312" RDEPEND="${DEPEND}" diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild deleted file mode 100644 index b9a50ebd1..000000000 --- a/sci-biology/salmon/salmon-0.3.2.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) - -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc - dev-cpp/tbb" -RDEPEND="${DEPEND}" - -src_install() { - cmake-utils_src_install - rm -r "${ED}"/usr/tests || die -} diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild deleted file mode 100644 index 42ccf1e6c..000000000 --- a/sci-biology/salmon/salmon-0.4.2.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch ) - -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc - dev-cpp/tbb" -RDEPEND="${DEPEND}" - -src_install() { - cmake-utils_src_install - rm -r "${ED}"/usr/tests || die -} diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild deleted file mode 100644 index 42ccf1e6c..000000000 --- a/sci-biology/salmon/salmon-0.5.0.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch ) - -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc - dev-cpp/tbb" -RDEPEND="${DEPEND}" - -src_install() { - cmake-utils_src_install - rm -r "${ED}"/usr/tests || die -} diff --git a/sci-biology/salmon/salmon-0.9.1.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild deleted file mode 100644 index 34a425403..000000000 --- a/sci-biology/salmon/salmon-0.9.1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon"; -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc - dev-cpp/tbb" -RDEPEND="${DEPEND}" - -src_install() { - cmake-utils_src_install - rm -r "${ED}"/usr/tests || die -} diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index ab0f9c368..0083648fb 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -8,15 +8,35 @@ 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 -> ${PN}-0.10.2_RapMap.zip" LICENSE="GPL-3" SLOT="0" IUSE="" -DEPEND="dev-libs/boost:0 - dev-libs/jemalloc +PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch + "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch ) + +# budled copies of: +# sci-biology/bwa-0.7.12.5 +# sci-biology/jellyfish +# sci-biology/staden-1.14.8.1 +# sci-biology/gfftools +# +# libgff-1.1 from https://github.com/Kingsford-Group/libgff +# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz +# https://github.com/Kingsford-Group/libgff/issues/1 +# +# dev-libs/spdlog-0.16.1 +# cereal-1.2.2 +DEPEND="sys-libs/zlib + app-arch/bzip2 + app-arch/xz-utils + dev-libs/boost:0[threads] + >=dev-libs/jemalloc-5.0.1 >=dev-cpp/tbb-2018.20180312" RDEPEND="${DEPEND}" + # https://github.com/COMBINE-lab/salmon/issues/19 # # contains bundled copies of https://github.com/jemalloc/jemalloc
