Adding metadata

6 files changed, 1 insertions, 199 deletions

diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 0b52182a52f6..4b33688aa042 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,2 +1 @@
-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-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild
deleted file mode 100644
index 7b5aa6f1fdab..000000000000
--- a/sci-biology/bedtools/bedtools-2.30.0.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
-
-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}"/${PN}-2.29.2-buildsystem.patch
-	"${FILESDIR}"/${PN}-2.29.2-python.patch
-	"${FILESDIR}"/${PN}-2.30.0-gcc13.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/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild
index 8892fbb37183..60febc1964f7 100644
--- a/sci-biology/bedtools/bedtools-2.31.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
deleted file mode 100644
index 573e88993bc9..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -4,44 +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 ($(VERBOSE),1)
- CCPREFIX =
--else
--CCPREFIX = @
--endif
- 
- OBJ_DIR	= obj
- BIN_DIR	= bin
- SRC_DIR	= src
- 
--CXX     = g++
--
--ifeq ($(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 \
-@@ -204,7 +189,7 @@
- 
- # 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-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
deleted file mode 100644
index 9576a78bd1dd..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -183,7 +168,7 @@
- 
- $(BIN_DIR)/intersectBed: | $(BIN_DIR)
- 	@echo "- Creating executables for old CLI."
--	@python scripts/makeBashScripts.py
-+	$(EPYTHON) scripts/makeBashScripts.py
- 	@chmod +x bin/*
- 	@echo "done."
- 
---- a/src/utils/BamTools/Makefile.frag
-+++ b/src/utils/BamTools/Makefile.frag
-@@ -1,4 +1,4 @@
- src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
- 
- src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
--	python $^ > $@
-+	$(EPYTHON) $^ > $@
---- a/test/bigchroms/test-bigchroms.sh
-+++ b/test/bigchroms/test-bigchroms.sh
-@@ -28,7 +28,7 @@
- rm obs
- 
- if [[ "$BT_NO_BIG_FILES" != "" ]]; then
--python make-big-chrom.py
-+${EPYTHON} 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 @@
- echo "fisher,shuffled"
- 
- for i in $(seq 1000); do
--    fisher=$(python ./sim.py | tail -1 | cut -f 2)
-+    fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2)
-     shuffle=$(bash shuf.sh)
-     echo "$fisher,$shuffle"
- done
diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
deleted file mode 100644
index c63faf31c851..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-https://github.com/arq5x/bedtools2/pull/1045
-
-From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001
-From: David Seifert <soap@gentoo.org>
-Date: Tue, 18 Apr 2023 11:59:58 +0200
-Subject: [PATCH] Add missing <cstdint> include
-
-* breaks build with GCC 13:
-  https://bugs.gentoo.org/895860
----
- src/utils/general/ParseTools.h | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
-index e056c149..3418eff1 100644
---- a/src/utils/general/ParseTools.h
-+++ b/src/utils/general/ParseTools.h
-@@ -16,6 +16,7 @@
- #include "string.h"
- #include <cstdio>
- #include <cstdlib>
-+#include <cstdint>
- 
- using namespace std;
-