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sci-biology/bedtools: drop 2.30.0
Signed-off-by: Alfred Wingate <parona@protonmail.com> Part-of: https://github.com/gentoo/gentoo/pull/41820 Closes: https://github.com/gentoo/gentoo/pull/41820 Signed-off-by: Sam James <sam@gentoo.org>
This commit is contained in:
Alfred Wingate
committed by
Sam James
Sam James
parent
0532f407cc
commit
2f6e857eed
@@ -1,2 +1 @@
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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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@@ -1,49 +0,0 @@
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# Copyright 1999-2023 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_{9..11} )
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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}"/${PN}-2.29.2-buildsystem.patch
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"${FILESDIR}"/${PN}-2.29.2-python.patch
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"${FILESDIR}"/${PN}-2.30.0-gcc13.patch
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)
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src_configure() {
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tc-export AR CC CXX RANLIB
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}
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src_install() {
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default
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insinto /usr/share/bedtools
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doins -r genomes
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}
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@@ -1,82 +0,0 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -4,44 +4,29 @@
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# (c) 2009 Aaron Quinlan
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# ==========================
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-SHELL := /bin/bash -e
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+SHELL := bash -e
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VERSION_FILE=./src/utils/version/version_git.h
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RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
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# define our object and binary directories
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-ifeq ($(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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-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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@@ -204,7 +189,7 @@
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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 = $(htslib_default_libs)
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prefix = /usr/local
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@@ -1,41 +0,0 @@
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--- a/Makefile
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+++ b/Makefile
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@@ -183,7 +168,7 @@
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$(BIN_DIR)/intersectBed: | $(BIN_DIR)
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@echo "- Creating executables for old CLI."
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- @python scripts/makeBashScripts.py
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+ $(EPYTHON) scripts/makeBashScripts.py
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@chmod +x bin/*
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@echo "done."
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--- a/src/utils/BamTools/Makefile.frag
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+++ b/src/utils/BamTools/Makefile.frag
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@@ -1,4 +1,4 @@
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src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
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src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
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- python $^ > $@
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+ $(EPYTHON) $^ > $@
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--- a/test/bigchroms/test-bigchroms.sh
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+++ b/test/bigchroms/test-bigchroms.sh
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@@ -28,7 +28,7 @@
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rm obs
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if [[ "$BT_NO_BIG_FILES" != "" ]]; then
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-python make-big-chrom.py
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+${EPYTHON} make-big-chrom.py
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echo -e " bigchroms.t03...big get fasta \c"
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$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 @@
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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=$(${EPYTHON} ./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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@@ -1,25 +0,0 @@
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https://github.com/arq5x/bedtools2/pull/1045
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From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001
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From: David Seifert <soap@gentoo.org>
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Date: Tue, 18 Apr 2023 11:59:58 +0200
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Subject: [PATCH] Add missing <cstdint> include
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* breaks build with GCC 13:
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https://bugs.gentoo.org/895860
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---
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src/utils/general/ParseTools.h | 1 +
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1 file changed, 1 insertion(+)
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diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
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index e056c149..3418eff1 100644
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--- a/src/utils/general/ParseTools.h
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+++ b/src/utils/general/ParseTools.h
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@@ -16,6 +16,7 @@
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#include "string.h"
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#include <cstdio>
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#include <cstdlib>
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+#include <cstdint>
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using namespace std;
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