6 files changed, 191 insertions, 47 deletions
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 8d91db427f4f..5258bcd3f805 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,6 @@
-DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
-DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
-EBUILD bedtools-2.26.0.ebuild 959 BLAKE2B c3d42f033913e18a9bd1f0b6f669a4000bc6b6892bbd5986a33a99ed496ae4af11b690f1c7c350644b62e77baef80a9eb52f15e87818a74b684d4fac816a2512 SHA512 a3914d04806fa4b3f14f83d91717d00fd183e1f6d4a39690ae04e7767791605a8e90d86cefc4deaa50327651c64125808658de4471f05df936c19e46768bf988
+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-2.29.2-samtools-1.10.patch 659 BLAKE2B 5ec159e0a9bc9f4b5d661bcf93ba8a0cd08f62e8e6d3f92229b71d5dfb122d89eb6a68637e12394e6082cf9be99014787f9a780f7fb547ec61f5f8b8d405713d SHA512 0160c54ad3781e17df53b2525cbf0e6b5d1ebf5ce07257b16c35eed525623aa46b5ee32f158ab64b2e18a283eba0f8331a521ac8382cc31ca03cd88d1376c057
+DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
+EBUILD bedtools-2.29.2.ebuild 1232 BLAKE2B 6e5204cbdae38787b2667fd383ee2c5f8dcd2f08569b2454280bfc1e8821dafe46dce4eb4ed4b3f55b22c19dea5705fea25816f93b449feea3163dac6667dbc5 SHA512 ba09db688e841fa10d65e19534b6c0d903352f5a04996bd451df5ada09f8379b6a0b8bdbbdedd7b5ecda51036bc6c37bc512dd9a4c321ade4fdca10f30407474
 MISC metadata.xml 406 BLAKE2B 5a16830031644c5087241b9e20afcb6315095c877e2b019eace76ee0602929c168c2273e27e99f03ca3c1a57db0bf728c2d8ccc39b7f80588bb215d1fd6a3ea6 SHA512 35a9b50a772503e6691faf1e2f1093bd6ffd5f6f5be08b1ad8581948f4f3e8fb7e54faa101cff757fc561ed71696253114c32fb6293df59cda3e8fd7c24d2bb0
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
deleted file mode 100644
index b062a6fef84d..000000000000
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit flag-o-matic 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}/${P}.tar.gz
-	https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-DEPEND="${PYTHON_DEPS}
-	test? (
-		sci-libs/htslib
-		sci-biology/samtools:0
-	)"
-RDEPEND="sys-libs/zlib"
-
-S="${WORKDIR}/${PN}2"
-
-DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
-
-src_configure() {
-	append-lfs-flags
-	export prefix="${EPREFIX}/usr"
-	tc-export AR CXX
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/${PN}
-	doins -r genomes
-}
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
new file mode 100644
index 000000000000..fbc1f3a9b4f9
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+
+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="
+	${PYTHON_DEPS}
+	test? ( >=sci-biology/samtools-1.10:0 )"
+
+S="${WORKDIR}"/${PN}2
+
+# bedtools2 has a *terrible* build system and development practices.
+# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
+# that make unbundling it nigh impossible. There are no signs of upstream porting
+# their fork to 1.10, which means we're stuck with the bundled version.
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
+	"${FILESDIR}"/${PN}-2.29.2-python.patch
+	"${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch
+)
+
+src_configure() {
+	tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+	default
+
+	insinto /usr/share/${PN}
+	doins -r genomes
+}
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
new file mode 100644
index 000000000000..573e88993bc9
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
@@ -0,0 +1,82 @@
+--- 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
new file mode 100644
index 000000000000..9576a78bd1dd
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
@@ -0,0 +1,41 @@
+--- 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-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
new file mode 100644
index 000000000000..7cc0e23de2d4
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
@@ -0,0 +1,13 @@
+--- a/test/intersect/new_test-intersect.sh
++++ b/test/intersect/new_test-intersect.sh
+@@ -975,8 +975,8 @@
+ #  Test intersect preserve the text header in bam
+ ############################################################
+ echo -e "    intersect.new.t78...\c"
+-echo -e "@HD     VN:1.5  SO:coordinate" > exp
+-echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
++echo -e "@HD	VN:1.5	SO:coordinate" > exp
++echo "@HD	VN:1.5	SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;