commit: 89b29b2a57824d3a32051c4f8aa2eae6eb21bfab Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 15:28:59 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 15:28:59 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89b29b2a
sci-biology/salmon: add version 1.4.0 Closes: https://github.com/gentoo/sci/pull/1013 Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/salmon/salmon-1.4.0.ebuild | 40 +++++++++++++++++ sci-biology/salmon/salmon-9999.ebuild | 81 ++++++++++------------------------ 2 files changed, 63 insertions(+), 58 deletions(-) diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild new file mode 100644 index 000000000..858ff642b --- /dev/null +++ b/sci-biology/salmon/salmon-1.4.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2021 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 -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" + +RDEPEND=" + dev-libs/boost:=[threads] + sys-libs/zlib +" + +DEPEND="${RDEPEND} + app-arch/bzip2 + app-arch/xz-utils + >=dev-libs/jemalloc-5.0.1 + >=dev-cpp/tbb-2018.20180312 + sci-biology/pufferfish + sci-libs/staden-io + sci-libs/libgff + dev-libs/cereal +" + +BDEPEND=" + app-arch/unzip + net-misc/curl +" + +PATCHES=( + "${FILESDIR}/${P}-do-not-fetch-pufferfish.patch" + "${FILESDIR}/${P}-allow-newer-boost.patch" +) diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index 8862ff790..b7d02edd7 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -1,69 +1,34 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit multilib cmake-utils git-r3 +inherit cmake 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 -> ${P}_RapMap.zip -# https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz -# https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz -# https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz -# https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz -# https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" LICENSE="GPL-3" SLOT="0" -IUSE="" -PATCHES=( "${FILESDIR}"/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 - "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch - "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) - -# budled copies of: -# sci-biology/bwa-0.7.12.5 -# sci-biology/jellyfish -# sci-biology/staden-1.14.8.1 -# sci-biology/gfftools -# -# libgff-1.1 from https://github.com/Kingsford-Group/libgff -# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -# https://github.com/Kingsford-Group/libgff/issues/1 -# -# dev-libs/spdlog-0.16.1 -# cereal-1.2.2 -DEPEND="net-misc/curl - app-arch/unzip - sys-libs/zlib - app-arch/bzip2 - app-arch/xz-utils - dev-libs/boost:0[threads] - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312" -RDEPEND="${DEPEND}" - -# https://github.com/COMBINE-lab/salmon/issues/19 -# -# contains bundled copies of https://github.com/jemalloc/jemalloc -# https://github.com/gabime/spdlog -# https://github.com/efficient/libcuckoo -# https://github.com/greg7mdp/sparsepp -# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it -# https://github.com/Kingsford-Group/libgff -# sci-libs/io_lib -# -# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158 -# modified bwa copy -# -# and maybe more - -# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian - -# see the many curl executions: -# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null +RDEPEND=" + dev-libs/boost:=[threads] + sys-libs/zlib +" + +DEPEND="${RDEPEND} + app-arch/bzip2 + app-arch/xz-utils + >=dev-libs/jemalloc-5.0.1 + >=dev-cpp/tbb-2018.20180312 + sci-biology/pufferfish + sci-libs/staden-io + sci-libs/libgff + dev-libs/cereal +" + +BDEPEND=" + app-arch/unzip + net-misc/curl +"
