From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 21797158087 for ; Tue, 25 Jan 2022 13:06:46 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 4869C2BC002; Tue, 25 Jan 2022 13:06:45 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7045B2BC005 for ; Tue, 25 Jan 2022 13:06:44 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 827E9342D5F for ; Tue, 25 Jan 2022 13:06:41 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 00E4C26D for ; Tue, 25 Jan 2022 13:06:40 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1643115959.5514f84d164bf7fb697b19eb7f7661e14ad0b718.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/salmon/files/salmon-1.6.0-find-boost.patch sci-biology/salmon/salmon-1.4.0.ebuild sci-biology/salmon/salmon-1.6.0.ebuild X-VCS-Directories: sci-biology/salmon/files/ sci-biology/salmon/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 5514f84d164bf7fb697b19eb7f7661e14ad0b718 X-VCS-Branch: master Date: Tue, 25 Jan 2022 13:06:40 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 31b300d7-18d6-4e00-b3b3-a59fdca12655 X-Archives-Hash: 02f6e67b873a3ab0e46e7bc6fb50b64e commit: 5514f84d164bf7fb697b19eb7f7661e14ad0b718 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 25 13:05:59 2022 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 25 13:05:59 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5514f84d sci-biology/salmon: bump to 1.6.0 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan gentoo.org> .../salmon/files/salmon-1.6.0-find-boost.patch | 116 +++++++++++++++++++++ sci-biology/salmon/salmon-1.4.0.ebuild | 38 ------- sci-biology/salmon/salmon-1.6.0.ebuild | 70 +++++++++++++ 3 files changed, 186 insertions(+), 38 deletions(-) diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch new file mode 100644 index 000000000..76ef25547 --- /dev/null +++ b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch @@ -0,0 +1,116 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1be02ab..48ffda2 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -428,9 +428,9 @@ endif() + ## + # Set the latest version and look for what we need + ## +-set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0") ++set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0") + if (NOT BOOST_RECONFIGURE) +-find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options) ++find_package(Boost 1.59.0 COMPONENTS ALL) + message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}") + message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}") + message("Boost_FOUND = ${Boost_FOUND}") +@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND) + endif() + + ## Try and find TBB first +-find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) ++find_package(TBB) + + ## NOTE: we actually require at least 2019 U4 or greater + ## since we are using tbb::global_control. However, they +@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) + ## source. Check before release if we can bump to the 2020 + ## version (requires having tbb 2020 for OSX). + if (${TBB_FOUND}) +- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0) + message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}") + set(TBB_TARGET_EXISTED TRUE) +- else() +- set(TBB_TARGET_EXISTED FALSE) +- endif() + else() + set(TBB_TARGET_EXISTED FALSE) + endif() +@@ -750,10 +746,6 @@ if(NOT libgff_FOUND) + message("Build system will compile libgff") + message("==================================================================") + externalproject_add(libgff +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz && +- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz && +- tar -xzvf libgff.tgz + ## + #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz + #DOWNLOAD_NAME libff.tgz +diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake +index c8b3eb5..b4c23da 100644 +--- a/cmake/Modules/FindTBB.cmake ++++ b/cmake/Modules/FindTBB.cmake +@@ -184,7 +184,6 @@ if(NOT TBB_FOUND) + ################################## + + if(TBB_INCLUDE_DIRS) +- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file) + string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1" + TBB_VERSION_MAJOR "${_tbb_version_file}") + string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1" +diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh +index d32e131..1b5cbf2 100755 +--- a/scripts/fetchPufferfish.sh ++++ b/scripts/fetchPufferfish.sh +@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) + EXTERNAL_DIR=${CURR_DIR}/../external + INSTALL_DIR=${CURR_DIR}/../external/install + +-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then +- rm -fr ${EXTERNAL_DIR}/pufferfish +-fi +- +-if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then +- rm -fr ${INSTALL_DIR}/include/pufferfish +-fi +- +-if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then +- rm -fr ${INSTALL_DIR}/src/pufferfish +-fi +- + SVER=salmon-v1.6.0 + #SVER=develop + #SVER=sketch-mode +@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0 + EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc + + mkdir -p ${EXTERNAL_DIR} +-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip +- +-hashcheck="" +-if exists sha256sum; then +- hashcheck="sha256sum" +-elif exists shasum; then +- hashcheck="shasum -a256" +-else +- unset hashcheck +-fi +- +-if [ -z "${hashcheck-}" ]; then +- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish"; +-else +- if [[ $SVER != develop ]]; then +- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; } +- else +- echo "not testing sha since pulling from develop" +- fi +-fi +- +- +-rm -fr ${EXTERNAL_DIR}/pufferfish +-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} +-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish + + mkdir -p ${INSTALL_DIR}/include/pufferfish + diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild deleted file mode 100644 index 420cb2ae2..000000000 --- a/sci-biology/salmon/salmon-1.4.0.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI="https://github.com/COMBINE-lab/${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 - 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-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild new file mode 100644 index 000000000..6c19ff58f --- /dev/null +++ b/sci-biology/salmon/salmon-1.6.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +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 -> ${P}.tar.gz + https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz + https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz +" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-libs/boost:= + sys-libs/zlib +" + +DEPEND="${RDEPEND} + app-arch/bzip2 + app-arch/xz-utils + >=dev-libs/jemalloc-5.0.1 + >=dev-cpp/tbb-2018.20180312 + dev-libs/cereal + sci-libs/io_lib[static-libs] +" + +BDEPEND=" + app-arch/unzip + net-misc/curl +" + +PATCHES=( + "${FILESDIR}/${P}-find-boost.patch" +) + +src_unpack() { + default + mkdir -p "${S}/external/install/lib" || die + mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die + mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die + ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die + ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die + ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die +} + +src_prepare() { + cmake_src_prepare + sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \ + -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \ + -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die +} + +src_configure() { + local mycmakeargs=( + -DFETCH_BOOST=FALSE + -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost" + -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64" + -DBoost_ALL_FOUND=TRUE + -Dboost_headers_FOUND=TRUE + -DBoost_FOUND=TRUE + ) + cmake_src_configure +}