From 6243676c91946098c06d42bc87b5eb99aac40bf0 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Thu, 25 Apr 2024 23:59:45 +0100 Subject: gentoo auto-resync : 25:04:2024 - 23:59:45 --- sci-biology/bedtools/Manifest | 5 + sci-biology/bedtools/bedtools-2.31.1.ebuild | 49 ++++++ .../files/bedtools-2.31.1-buildsystem.patch | 84 ++++++++++ .../bedtools/files/bedtools-2.31.1-includes.patch | 180 +++++++++++++++++++++ .../bedtools/files/bedtools-2.31.1-python.patch | 42 +++++ 5 files changed, 360 insertions(+) create mode 100644 sci-biology/bedtools/bedtools-2.31.1.ebuild create mode 100644 sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch create mode 100644 sci-biology/bedtools/files/bedtools-2.31.1-includes.patch create mode 100644 sci-biology/bedtools/files/bedtools-2.31.1-python.patch (limited to 'sci-biology/bedtools') diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index b982e0eec460..19bc1abee266 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,6 +1,11 @@ AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85 AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f AUX bedtools-2.30.0-gcc13.patch 684 BLAKE2B 4c3a338887b5c71be1b096389e6c967aaf55de518663c4c3b5c37f80e6d651c6f8cf07c507064f8fe0f7bada66191d56dc136e71a5cb4254570c24ad8d8a1801 SHA512 a68f224a5b04f1b0949f8bd064c6847c0f5da900ac462fbfa2fe473688ce4e6c904ae94581599ecc0fe0a3baf0038effc8346c39dd4ecf7e068c449482594711 +AUX bedtools-2.31.1-buildsystem.patch 2090 BLAKE2B 0d75f27710d4fccb530f1477aa6a8f07a7ca92ba4b2608bd1a3733d5aa835bfbe75db6f512aee48bdaadc6826efdbe0719614a79b5bc67d5844624f16e4221f3 SHA512 7fe80cc622b41ed9efdca3ed4ccd33389352171b93974c04a6b0f588609582f0fd3b2c039e076a66773a2c9e21f9792c1c6876198744f974b66c0d5733caf7d4 +AUX bedtools-2.31.1-includes.patch 4556 BLAKE2B 7604ff9b20b8634ce1d0ca4684f5e7719b537a36e3a7bba758383cec9a40180db5d8a40f16f53bcc3c92783182e148fbb24de271653fb08965f9880bbb95b691 SHA512 53813f21545bc66210f63edfdebe9f5b302af5bdd16c6d79165a91e432bd89524fd8e203bdf67f25a54a57a9112f0b1ef96046e24469f0e452740cd3d3f0482e +AUX bedtools-2.31.1-python.patch 1357 BLAKE2B 7931decea602f2de399789708545797493428c37cf83121fd88d8be7075e3758038b7e9138cf9a7c063801de886530b389d9c100abe414a3f1879c449d0eb3f9 SHA512 8b0bd9e122035abb479fe3d27eec592e22ebf8a71fcab04469b3d60a86f88d16c818a5091c7390c46db86e5c78743e4171b827167b316dd2352175802cdea291 DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 +DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d EBUILD bedtools-2.30.0.ebuild 1227 BLAKE2B f54a0f5f84ade175cd07634d657b970a05b864606c76b80fac8dc3d037398c9611a5fc4c5fd7514e329e8375aa59522fd094e70c9d151af318708fc1c8bd7bbe SHA512 c3318eff7f9363f5a803b85d5d092d085b9e4198051d79d314c390d7200398989127b9a501459185497859f57352e4416fb5210f6d647ea76793a395c69f223f +EBUILD bedtools-2.31.1.ebuild 1231 BLAKE2B 8d1ad16ff5d59f4902f4c5e8801ec8fedd32b4b41c30dae78f1a041a91c7b821e293c7a4a20add9ae9c72d1883a24f364c9c688eee7302dc8da06eedbd375efd SHA512 02bcc98256e48d81a4362c6e231d97ff98c6a15190cd6105538701639fea2fcc50921489bd49edd284b2a950a5e74a082981bb6ebc513805d5c124ee680c5a8a MISC metadata.xml 407 BLAKE2B f3c2890ef1648dcfc7ae92c56fec8c111de2cb82ba4c8f7402756fa9db6f2ee43fa3ccb9a75db5d1e2ca7893ed3041efc22452814944e0e56f1a589353b47774 SHA512 925406053fd5c1aecb5ef26c522b3f410c6f9a639dc1ab7790a4124513c870af5b818adc53875c93ab19a36d444b8fb23c5ef10cc11ed50080785bbe60d1eb98 diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild new file mode 100644 index 000000000000..57ee6c3fde3f --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" +S="${WORKDIR}/${PN}2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.31.1-buildsystem.patch + "${FILESDIR}"/${PN}-2.31.1-python.patch + "${FILESDIR}"/${PN}-2.31.1-includes.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/bedtools + doins -r genomes +} diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch new file mode 100644 index 000000000000..8bb2a096e917 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch @@ -0,0 +1,84 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,46 +4,29 @@ + # (c) 2009 Aaron Quinlan + # ========================== + +-SHELL := /bin/bash -e ++SHELL := bash -e + + VERSION_FILE=./src/utils/version/version_git.h + RELEASED_VERSION_FILE=./src/utils/version/version_release.txt + + + # define our object and binary directories +-ifeq ($(VERBOSE),1) + CCPREFIX = +-else +-CCPREFIX = @ +-endif + + OBJ_DIR = obj + BIN_DIR = bin + SRC_DIR = src + +-CXX = g++ +- +-PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3) +- +-ifeq ($(DEBUG),1) +-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0 +-else + BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) +-BT_CXXFLAGS = -g -Wall -O2 +-endif ++BT_CXXFLAGS = -Wall + + # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). +-ifeq ($(USE_RAND),1) +-BT_CXXFLAGS += -DUSE_RAND +-else + BT_CXXFLAGS += -std=c++11 +-endif + + BT_LDFLAGS = + BT_LIBS = -lz -lm -lbz2 -llzma -lpthread + +-prefix ?= /usr/local ++prefix = $(EPREFIX)/usr + + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ +@@ -213,7 +196,7 @@ + + # make the "obj/" and "bin/" directories, if they don't exist + $(OBJ_DIR) $(BIN_DIR): +- @mkdir -p $@ ++ mkdir -p $@ + + + # Usually HTSlib's configure script has not been used (detected via config.mk +--- a/src/utils/htslib/Makefile ++++ b/src/utils/htslib/Makefile +@@ -22,20 +22,13 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib +- + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = + LIBS = $(htslib_default_libs) + + prefix = /usr/local diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch new file mode 100644 index 000000000000..927b1b944d6e --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch @@ -0,0 +1,180 @@ +https://github.com/arq5x/bedtools2/pull/1087 + +From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001 +From: David Seifert +Date: Thu, 25 Apr 2024 11:18:48 +0200 +Subject: [PATCH] Add missing `stdint.h` includes + +* Musl is a lot stricter with transitive includes: + Bug: https://bugs.gentoo.org/907971 +--- a/src/bamToBed/bamToBed.cpp ++++ b/src/bamToBed/bamToBed.cpp +@@ -22,6 +22,7 @@ using namespace BamTools; + #include + #include + #include ++#include + + using namespace std; + +--- a/src/clusterBed/clusterBed.cpp ++++ b/src/clusterBed/clusterBed.cpp +@@ -12,6 +12,8 @@ + #include "lineFileUtilities.h" + #include "clusterBed.h" + ++#include ++ + // = Constructor = + BedCluster::BedCluster(string &bedFile, + int maxDistance, +--- a/src/pairToBed/pairToBed.h ++++ b/src/pairToBed/pairToBed.h +@@ -22,6 +22,7 @@ using namespace BamTools; + #include + #include + #include ++#include + + using namespace std; + +--- a/src/randomBed/randomBed.h ++++ b/src/randomBed/randomBed.h +@@ -22,6 +22,7 @@ + #include + #include + #include // for binary search ++#include + using namespace std; + + const int MAX_TRIES = 1000000; +--- a/src/summaryFile/summaryFile.h ++++ b/src/summaryFile/summaryFile.h +@@ -12,6 +12,8 @@ + #include "ToolBase.h" + #include "ContextSummary.h" + ++#include ++ + struct Interval { + CHRPOS start; + CHRPOS end; +--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp ++++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp +@@ -1,3 +1,4 @@ ++#include + + struct _RefID_t { + operator int32_t() const {return (int32_t)(_ptr()->core.tid);} +--- a/src/utils/BamTools/include/api/BamAux.h ++++ b/src/utils/BamTools/include/api/BamAux.h +@@ -1,4 +1,5 @@ + #include ++#include + + #ifndef BAMAUX_H + #define BAMAUX_H +--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h ++++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h +@@ -9,6 +9,7 @@ + #define SINGLELINETEXTFILEREADER_H_ + + #include ++#include + #include "FileReader.h" + #include "string.h" + #include "lineFileUtilities.h" +--- a/src/utils/FileRecordTools/Records/BamRecord.cpp ++++ b/src/utils/FileRecordTools/Records/BamRecord.cpp +@@ -10,6 +10,8 @@ + #include "BamFileReader.h" + #include "RecordKeyVector.h" + ++#include ++ + BamRecord::BamRecord() + : _bamChromId(-1) + { +--- a/src/utils/GenomeFile/GenomeFile.h ++++ b/src/utils/GenomeFile/GenomeFile.h +@@ -19,6 +19,7 @@ + #include + #include + #include ++#include + #include // for bsearch lower_bound() + #include "api/BamReader.h" + #include "api/BamAux.h" +--- a/src/utils/GenomeFile/NewGenomeFile.h ++++ b/src/utils/GenomeFile/NewGenomeFile.h +@@ -14,6 +14,7 @@ + #define NEW_GENOMEFILE_H + + #include // for bsearch lower_bound() ++#include + + #include "BedtoolsTypes.h" + +--- a/src/utils/bedFilePE/bedFilePE.h ++++ b/src/utils/bedFilePE/bedFilePE.h +@@ -8,6 +8,7 @@ + #include + #include + #include ++#include + #include + #include "bedFile.h" + #include "lineFileUtilities.h" +--- a/src/utils/general/ParseTools.cpp ++++ b/src/utils/general/ParseTools.cpp +@@ -2,7 +2,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include +--- a/src/utils/lineFileUtilities/lineFileUtilities.h ++++ b/src/utils/lineFileUtilities/lineFileUtilities.h +@@ -4,6 +4,7 @@ + #include + #include + #include ++#include + #include + #include + #include +--- a/src/utils/sequenceUtilities/sequenceUtils.h ++++ b/src/utils/sequenceUtilities/sequenceUtils.h +@@ -4,6 +4,7 @@ + #include + #include + #include ++#include + + using namespace std; + +--- a/src/windowMaker/windowMaker.h ++++ b/src/windowMaker/windowMaker.h +@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license. + #include "NewGenomeFile.h" + #include "bedFile.h" + ++#include ++ + using namespace std; + + +--- a/src/windowMaker/windowMakerMain.cpp ++++ b/src/windowMaker/windowMakerMain.cpp +@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license. + #include "windowMaker.h" + #include "version.h" + ++#include ++ + using namespace std; + + // define our program name diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-python.patch b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch new file mode 100644 index 000000000000..99fc1b1d480b --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch @@ -0,0 +1,42 @@ +https://github.com/arq5x/bedtools2/pull/1087 + +From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001 +From: David Seifert +Date: Thu, 25 Apr 2024 11:18:47 +0200 +Subject: [PATCH] Allow PYTHON from environment + +* Distros need to be able to specify exactly which python + interpreter to run tests under. +--- a/test/bigchroms/test-bigchroms.sh ++++ b/test/bigchroms/test-bigchroms.sh +@@ -28,7 +28,7 @@ check obs abig.bed + rm obs + + if [[ "$BT_NO_BIG_FILES" != "" ]]; then +-python make-big-chrom.py ++${PYTHON:-python} make-big-chrom.py + + echo -e " bigchroms.t03...big get fasta \c" + $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs +--- a/test/fisher/cmp.sh ++++ b/test/fisher/cmp.sh +@@ -3,7 +3,7 @@ set -eo pipefail + echo "fisher,shuffled" + + for i in $(seq 1000); do +- fisher=$(python ./sim.py | tail -1 | cut -f 2) ++ fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2) + shuffle=$(bash shuf.sh) + echo "$fisher,$shuffle" + done +--- a/test/genomecov/test-genomecov.sh ++++ b/test/genomecov/test-genomecov.sh +@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs + check obs exp + rm obs exp + +-python mk-deep.py > deep.sam ++${PYTHON:-python} mk-deep.py > deep.sam + echo -e " genomecov.t18...\c" + echo "c1 1 1000000" > exp + $BT genomecov -d -ibam deep.sam | head -1 > obs -- cgit v1.2.3