commit: 6659d55f12a3e8b75dbf9545cac23f37ca00bd58 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Apr 25 09:37:47 2024 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Apr 25 09:37:47 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6659d55f
sci-biology/bedtools: add 2.31.1 Bug: https://bugs.gentoo.org/881783 Bug: https://bugs.gentoo.org/907971 Bug: https://bugs.gentoo.org/929751 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bedtools/Manifest | 1 + 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 | 178 +++++++++++++++++++++ .../bedtools/files/bedtools-2.31.1-python.patch | 40 +++++ 5 files changed, 352 insertions(+) diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 571c4c92d6b5..0b52182a52f6 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1 +1,2 @@ DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 +DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d 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..1b0a9f0849ed --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch @@ -0,0 +1,178 @@ +From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001 +From: David Seifert <[email protected]> +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 <sstream> + #include <fstream> + #include <stdlib.h> ++#include <stdint.h> + + using namespace std; + +--- a/src/clusterBed/clusterBed.cpp ++++ b/src/clusterBed/clusterBed.cpp +@@ -12,6 +12,8 @@ + #include "lineFileUtilities.h" + #include "clusterBed.h" + ++#include <stdint.h> ++ + // = 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 <vector> + #include <iostream> + #include <fstream> ++#include <stdint.h> + + using namespace std; + +--- a/src/randomBed/randomBed.h ++++ b/src/randomBed/randomBed.h +@@ -22,6 +22,7 @@ + #include <unistd.h> + #include <sys/types.h> + #include <algorithm> // for binary search ++#include <stdint.h> + 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 <stdint.h> ++ + 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 <stdint.h> + + 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 <string> ++#include <stdint.h> + + #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 <algorithm> ++#include <stdint.h> + #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 <stdint.h> ++ + BamRecord::BamRecord() + : _bamChromId(-1) + { +--- a/src/utils/GenomeFile/GenomeFile.h ++++ b/src/utils/GenomeFile/GenomeFile.h +@@ -19,6 +19,7 @@ + #include <fstream> + #include <cstring> + #include <cstdio> ++#include <stdint.h> + #include <algorithm> // 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 <algorithm> // for bsearch lower_bound() ++#include <stdint.h> + + #include "BedtoolsTypes.h" + +--- a/src/utils/bedFilePE/bedFilePE.h ++++ b/src/utils/bedFilePE/bedFilePE.h +@@ -8,6 +8,7 @@ + #include <fstream> + #include <sstream> + #include <cstring> ++#include <stdint.h> + #include <algorithm> + #include "bedFile.h" + #include "lineFileUtilities.h" +--- a/src/utils/general/ParseTools.cpp ++++ b/src/utils/general/ParseTools.cpp +@@ -2,7 +2,7 @@ + #include <climits> + #include <cctype> + #include <cstring> +-#include <cstdint> ++#include <stdint.h> + #include <cstdio> + #include <cstdlib> + #include <sstream> +--- a/src/utils/lineFileUtilities/lineFileUtilities.h ++++ b/src/utils/lineFileUtilities/lineFileUtilities.h +@@ -4,6 +4,7 @@ + #include <vector> + #include <string> + #include <cstring> ++#include <stdint.h> + #include <cstdlib> + #include <sstream> + #include <iostream> +--- a/src/utils/sequenceUtilities/sequenceUtils.h ++++ b/src/utils/sequenceUtilities/sequenceUtils.h +@@ -4,6 +4,7 @@ + #include <string> + #include <algorithm> + #include <cctype> ++#include <stdint.h> + + 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 <stdint.h> ++ + 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 <stdint.h> ++ + 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..28819ac82d49 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch @@ -0,0 +1,40 @@ +From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001 +From: David Seifert <[email protected]> +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
