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commit: 3a1f5a9faf6dfeb828e148cd397290d670c93744 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Aug 16 20:49:49 2020 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Aug 16 20:49:49 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3a1f5a9f |
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|
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sci-biology/bedtools: Version bump to 2.29.2 |
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|
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Bug: https://bugs.gentoo.org/718468 |
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Package-Manager: Portage-3.0.2, Repoman-2.3.23 |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/bedtools/Manifest | 1 + |
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sci-biology/bedtools/bedtools-2.29.2.ebuild | 48 +++++++++++++ |
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.../files/bedtools-2.29.2-buildsystem.patch | 82 ++++++++++++++++++++++ |
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.../bedtools/files/bedtools-2.29.2-python.patch | 41 +++++++++++ |
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.../files/bedtools-2.29.2-samtools-1.10.patch | 13 ++++ |
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5 files changed, 185 insertions(+) |
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|
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diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest |
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index 642fe852658..d776ef0925a 100644 |
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--- a/sci-biology/bedtools/Manifest |
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+++ b/sci-biology/bedtools/Manifest |
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@@ -1,2 +1,3 @@ |
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DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 |
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DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def |
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+DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5 |
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|
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diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild |
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new file mode 100644 |
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index 00000000000..de337827bf2 |
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--- /dev/null |
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+++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild |
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@@ -0,0 +1,48 @@ |
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+# Copyright 1999-2020 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+ |
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+PYTHON_COMPAT=( python3_{6..9} ) |
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+ |
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+inherit python-any-r1 toolchain-funcs |
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+ |
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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}/${P}.tar.gz" |
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+ |
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+LICENSE="GPL-2" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="test" |
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+RESTRICT="!test? ( test )" |
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+ |
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+RDEPEND=" |
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+ app-arch/bzip2 |
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+ app-arch/xz-utils |
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+ sys-libs/zlib" |
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+DEPEND="${RDEPEND}" |
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+BDEPEND="test? ( >=sci-biology/samtools-1.10:0 )" |
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+ |
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+S="${WORKDIR}"/${PN}2 |
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+ |
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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}-2.29.2-samtools-1.10.patch |
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+) |
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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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+ |
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+src_install() { |
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+ default |
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+ |
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+ insinto /usr/share/${PN} |
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+ doins -r genomes |
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+} |
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|
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diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch |
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new file mode 100644 |
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index 00000000000..573e88993bc |
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--- /dev/null |
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+++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch |
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@@ -0,0 +1,82 @@ |
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+--- a/Makefile |
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++++ b/Makefile |
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+@@ -4,44 +4,29 @@ |
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+ # (c) 2009 Aaron Quinlan |
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+ # ========================== |
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+ |
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+-SHELL := /bin/bash -e |
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++SHELL := bash -e |
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+ |
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+ VERSION_FILE=./src/utils/version/version_git.h |
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+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt |
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+ |
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+ |
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+ # define our object and binary directories |
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+-ifeq ($(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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+ |
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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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+ |
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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 $(INCLUDES) |
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+-BT_CXXFLAGS = -g -Wall -O2 |
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+-endif |
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++BT_CXXFLAGS = -Wall |
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+ |
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+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). |
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+-ifeq ($(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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+ |
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+ BT_LDFLAGS = |
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+ BT_LIBS = -lz -lm -lbz2 -llzma -lpthread |
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+ |
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+-prefix ?= /usr/local |
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++prefix = $(EPREFIX)/usr |
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+ |
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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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+ |
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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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+ |
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+ |
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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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+ |
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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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+ |
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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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+ |
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+ prefix = /usr/local |
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|
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diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch |
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new file mode 100644 |
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index 00000000000..9576a78bd1d |
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--- /dev/null |
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+++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch |
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@@ -0,0 +1,41 @@ |
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+--- a/Makefile |
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++++ b/Makefile |
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+@@ -183,7 +168,7 @@ |
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+ |
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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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+ |
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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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+ |
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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) $^ > $@ |
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+--- a/test/bigchroms/test-bigchroms.sh |
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++++ b/test/bigchroms/test-bigchroms.sh |
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+@@ -28,7 +28,7 @@ |
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+ rm obs |
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+ |
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+ if [[ "$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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+ |
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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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+ |
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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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|
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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 |
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new file mode 100644 |
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index 00000000000..7cc0e23de2d |
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--- /dev/null |
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+++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch |
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@@ -0,0 +1,13 @@ |
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+--- a/test/intersect/new_test-intersect.sh |
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++++ b/test/intersect/new_test-intersect.sh |
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+@@ -975,8 +975,8 @@ |
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+ # Test intersect preserve the text header in bam |
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+ ############################################################ |
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+ echo -e " intersect.new.t78...\c" |
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+-echo -e "@HD VN:1.5 SO:coordinate" > exp |
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+-echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs |
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++echo -e "@HD VN:1.5 SO:coordinate" > exp |
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++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 |
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+ check exp obs |
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+ rm exp obs |
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+ [[ $FAILURES -eq 0 ]] || exit 1; |