diff options
Diffstat (limited to 'sci-biology/salmon/salmon-0.10.2.ebuild')
| -rw-r--r-- | sci-biology/salmon/salmon-0.10.2.ebuild | 73 |
1 files changed, 0 insertions, 73 deletions
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild deleted file mode 100644 index c3ef9e50a..000000000 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -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 - https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip - https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz - https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz - https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz - https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${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 - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch - "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) - -RDEPEND="${DEPEND}" -# budled copies of: -# sci-biology/bwa-0.7.12.5 -# sci-biology/jellyfish -# sci-biology/staden-1.14.8.1 -# sci-biology/gfftools -# -# libgff-1.1 from https://github.com/Kingsford-Group/libgff -# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -# https://github.com/Kingsford-Group/libgff/issues/1 -# -# dev-libs/spdlog-0.16.1 -# cereal-1.2.2 - -# see the many curl executions: -# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null -# -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - app-arch/xz-utils - dev-libs/boost:0= - dev-libs/libdivsufsort - sci-biology/bwa - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 -" -RDEPEND="${DEPEND}" -BDEPEND=" - net-misc/curl - app-arch/unzip -" - -src_prepare() { - # use system libs - sed -i \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(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 -} |