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@gentoo.org>
This commit is contained in:
David Seifert
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7f6851b030
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DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
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DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d
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@ -0,0 +1,49 @@
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# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{10..12} )
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inherit python-any-r1 toolchain-funcs
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DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
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HOMEPAGE="https://bedtools.readthedocs.io/"
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SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
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S="${WORKDIR}/${PN}2"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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RESTRICT="!test? ( test )"
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RDEPEND="
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app-arch/bzip2
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app-arch/xz-utils
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sys-libs/zlib"
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DEPEND="${RDEPEND}"
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BDEPEND="
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${PYTHON_DEPS}
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test? ( >=sci-biology/samtools-1.10:0 )"
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# bedtools2 has a *terrible* build system and development practices.
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# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
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# that make unbundling it nigh impossible. There are no signs of upstream porting
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# their fork to 1.10, which means we're stuck with the bundled version.
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PATCHES=(
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"${FILESDIR}"/${PN}-2.31.1-buildsystem.patch
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"${FILESDIR}"/${PN}-2.31.1-python.patch
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"${FILESDIR}"/${PN}-2.31.1-includes.patch
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)
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src_configure() {
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tc-export AR CC CXX RANLIB
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}
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src_install() {
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default
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insinto /usr/share/bedtools
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doins -r genomes
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}
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@ -0,0 +1,84 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -4,46 +4,29 @@
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# (c) 2009 Aaron Quinlan
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# ==========================
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-SHELL := /bin/bash -e
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+SHELL := bash -e
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VERSION_FILE=./src/utils/version/version_git.h
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RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
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# define our object and binary directories
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-ifeq ($(VERBOSE),1)
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CCPREFIX =
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-else
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-CCPREFIX = @
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-endif
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OBJ_DIR = obj
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BIN_DIR = bin
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SRC_DIR = src
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-CXX = g++
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-
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-PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
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-
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-ifeq ($(DEBUG),1)
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-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
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-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
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-else
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BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
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-BT_CXXFLAGS = -g -Wall -O2
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-endif
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+BT_CXXFLAGS = -Wall
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# If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
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-ifeq ($(USE_RAND),1)
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-BT_CXXFLAGS += -DUSE_RAND
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-else
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BT_CXXFLAGS += -std=c++11
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-endif
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BT_LDFLAGS =
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BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
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-prefix ?= /usr/local
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+prefix = $(EPREFIX)/usr
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SUBDIRS = $(SRC_DIR)/annotateBed \
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$(SRC_DIR)/bamToBed \
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@@ -213,7 +196,7 @@
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# make the "obj/" and "bin/" directories, if they don't exist
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$(OBJ_DIR) $(BIN_DIR):
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- @mkdir -p $@
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+ mkdir -p $@
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# Usually HTSlib's configure script has not been used (detected via config.mk
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--- a/src/utils/htslib/Makefile
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+++ b/src/utils/htslib/Makefile
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@@ -22,20 +22,13 @@
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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-CC = gcc
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-AR = ar
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-RANLIB = ranlib
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-
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# Default libraries to link if configure is not used
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htslib_default_libs = -lz -lm -lbz2 -llzma
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-CPPFLAGS =
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# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
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# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
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#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
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-CFLAGS = -g -Wall -O2
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EXTRA_CFLAGS_PIC = -fpic
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-LDFLAGS =
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LIBS = $(htslib_default_libs)
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prefix = /usr/local
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@ -0,0 +1,178 @@
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From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001
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From: David Seifert <soap@gentoo.org>
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Date: Thu, 25 Apr 2024 11:18:48 +0200
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Subject: [PATCH] Add missing `stdint.h` includes
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* Musl is a lot stricter with transitive includes:
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Bug: https://bugs.gentoo.org/907971
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--- a/src/bamToBed/bamToBed.cpp
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+++ b/src/bamToBed/bamToBed.cpp
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@@ -22,6 +22,7 @@ using namespace BamTools;
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#include <sstream>
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#include <fstream>
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#include <stdlib.h>
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+#include <stdint.h>
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using namespace std;
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--- a/src/clusterBed/clusterBed.cpp
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+++ b/src/clusterBed/clusterBed.cpp
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@@ -12,6 +12,8 @@
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#include "lineFileUtilities.h"
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#include "clusterBed.h"
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+#include <stdint.h>
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+
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// = Constructor =
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BedCluster::BedCluster(string &bedFile,
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int maxDistance,
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--- a/src/pairToBed/pairToBed.h
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+++ b/src/pairToBed/pairToBed.h
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@@ -22,6 +22,7 @@ using namespace BamTools;
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#include <vector>
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#include <iostream>
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#include <fstream>
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+#include <stdint.h>
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using namespace std;
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--- a/src/randomBed/randomBed.h
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+++ b/src/randomBed/randomBed.h
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@@ -22,6 +22,7 @@
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#include <unistd.h>
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#include <sys/types.h>
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#include <algorithm> // for binary search
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+#include <stdint.h>
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using namespace std;
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const int MAX_TRIES = 1000000;
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--- a/src/summaryFile/summaryFile.h
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+++ b/src/summaryFile/summaryFile.h
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@@ -12,6 +12,8 @@
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#include "ToolBase.h"
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#include "ContextSummary.h"
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+#include <stdint.h>
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+
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struct Interval {
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CHRPOS start;
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CHRPOS end;
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--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp
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+++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp
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@@ -1,3 +1,4 @@
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+#include <stdint.h>
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struct _RefID_t {
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operator int32_t() const {return (int32_t)(_ptr()->core.tid);}
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--- a/src/utils/BamTools/include/api/BamAux.h
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+++ b/src/utils/BamTools/include/api/BamAux.h
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@@ -1,4 +1,5 @@
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#include <string>
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+#include <stdint.h>
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#ifndef BAMAUX_H
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#define BAMAUX_H
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--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
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+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
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@@ -9,6 +9,7 @@
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#define SINGLELINETEXTFILEREADER_H_
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#include <algorithm>
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+#include <stdint.h>
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#include "FileReader.h"
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#include "string.h"
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#include "lineFileUtilities.h"
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--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
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+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
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@@ -10,6 +10,8 @@
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#include "BamFileReader.h"
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#include "RecordKeyVector.h"
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+#include <stdint.h>
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+
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BamRecord::BamRecord()
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: _bamChromId(-1)
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{
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--- a/src/utils/GenomeFile/GenomeFile.h
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+++ b/src/utils/GenomeFile/GenomeFile.h
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@@ -19,6 +19,7 @@
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#include <fstream>
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#include <cstring>
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#include <cstdio>
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+#include <stdint.h>
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#include <algorithm> // for bsearch lower_bound()
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#include "api/BamReader.h"
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#include "api/BamAux.h"
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--- a/src/utils/GenomeFile/NewGenomeFile.h
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+++ b/src/utils/GenomeFile/NewGenomeFile.h
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@@ -14,6 +14,7 @@
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#define NEW_GENOMEFILE_H
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#include <algorithm> // for bsearch lower_bound()
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+#include <stdint.h>
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#include "BedtoolsTypes.h"
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--- a/src/utils/bedFilePE/bedFilePE.h
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+++ b/src/utils/bedFilePE/bedFilePE.h
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@@ -8,6 +8,7 @@
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#include <fstream>
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#include <sstream>
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#include <cstring>
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+#include <stdint.h>
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#include <algorithm>
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#include "bedFile.h"
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#include "lineFileUtilities.h"
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--- a/src/utils/general/ParseTools.cpp
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+++ b/src/utils/general/ParseTools.cpp
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@@ -2,7 +2,7 @@
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#include <climits>
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#include <cctype>
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#include <cstring>
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-#include <cstdint>
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+#include <stdint.h>
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#include <cstdio>
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#include <cstdlib>
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#include <sstream>
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--- a/src/utils/lineFileUtilities/lineFileUtilities.h
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+++ b/src/utils/lineFileUtilities/lineFileUtilities.h
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@@ -4,6 +4,7 @@
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#include <vector>
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#include <string>
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#include <cstring>
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+#include <stdint.h>
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#include <cstdlib>
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#include <sstream>
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#include <iostream>
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--- a/src/utils/sequenceUtilities/sequenceUtils.h
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+++ b/src/utils/sequenceUtilities/sequenceUtils.h
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@@ -4,6 +4,7 @@
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#include <string>
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#include <algorithm>
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#include <cctype>
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+#include <stdint.h>
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using namespace std;
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--- a/src/windowMaker/windowMaker.h
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+++ b/src/windowMaker/windowMaker.h
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@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
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#include "NewGenomeFile.h"
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#include "bedFile.h"
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+#include <stdint.h>
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+
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using namespace std;
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--- a/src/windowMaker/windowMakerMain.cpp
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+++ b/src/windowMaker/windowMakerMain.cpp
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@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
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#include "windowMaker.h"
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#include "version.h"
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+#include <stdint.h>
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+
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using namespace std;
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// define our program name
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@ -0,0 +1,40 @@
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From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001
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From: David Seifert <soap@gentoo.org>
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Date: Thu, 25 Apr 2024 11:18:47 +0200
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Subject: [PATCH] Allow PYTHON from environment
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* Distros need to be able to specify exactly which python
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interpreter to run tests under.
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--- a/test/bigchroms/test-bigchroms.sh
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+++ b/test/bigchroms/test-bigchroms.sh
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@@ -28,7 +28,7 @@ check obs abig.bed
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rm obs
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if [[ "$BT_NO_BIG_FILES" != "" ]]; then
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-python make-big-chrom.py
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+${PYTHON:-python} make-big-chrom.py
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echo -e " bigchroms.t03...big get fasta \c"
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$BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
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--- a/test/fisher/cmp.sh
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+++ b/test/fisher/cmp.sh
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@@ -3,7 +3,7 @@ set -eo pipefail
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echo "fisher,shuffled"
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for i in $(seq 1000); do
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- fisher=$(python ./sim.py | tail -1 | cut -f 2)
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+ fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2)
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shuffle=$(bash shuf.sh)
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echo "$fisher,$shuffle"
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done
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--- a/test/genomecov/test-genomecov.sh
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+++ b/test/genomecov/test-genomecov.sh
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@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs
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check obs exp
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rm obs exp
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-python mk-deep.py > deep.sam
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+${PYTHON:-python} mk-deep.py > deep.sam
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echo -e " genomecov.t18...\c"
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echo "c1 1 1000000" > exp
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$BT genomecov -d -ibam deep.sam | head -1 > obs
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