commit: 4647f40e12c546cd0b18b1966acd944fc8a21641 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 31 21:00:05 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 31 21:00:05 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4647f40e
Revert "sci-biology/deeptools: add a new package" This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd. dev-python/pyBigWig/metadata.xml | 12 ---- dev-python/pyBigWig/pyBigWig-0.3.4.ebuild | 16 ----- dev-python/pyBigWig/pyBigWig-9999.ebuild | 18 ------ sci-biology/deeptools/deeptools-2.5.0.ebuild | 33 ---------- sci-biology/deeptools/deeptools-9999.ebuild | 34 ---------- sci-biology/deeptools/metadata.xml | 12 ---- sci-biology/mira/mira-4.9.6.ebuild | 93 ---------------------------- sci-biology/plinkseq/plinkseq-9999.ebuild | 13 ++-- 8 files changed, 5 insertions(+), 226 deletions(-) diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml deleted file mode 100644 index f68a1b6fa..000000000 --- a/dev-python/pyBigWig/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild deleted file mode 100644 index 33664c388..000000000 --- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild +++ /dev/null @@ -1,16 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files" -HOMEPAGE="https://github.com/dpryan79/pyBigWig"; -SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-biology/libBigWig" -RDEPEND="${DEPEND}" diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild deleted file mode 100644 index 0e2cd40c8..000000000 --- a/dev-python/pyBigWig/pyBigWig-9999.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit git-r3 - -DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files" -HOMEPAGE="https://github.com/dpryan79/pyBigWig"; -EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/libBigWig" -RDEPEND="${DEPEND}" diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild deleted file mode 100644 index 6f9a41d54..000000000 --- a/sci-biology/deeptools/deeptools-2.5.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 python3_5 ) - -inherit distutils-r1 - -[ "$PV" == "9999" ] && inherit git-2 - -DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" -HOMEPAGE="https://github.com/fidelram/deepTools"; -if [ "$PV" == "9999" ]; then - EGIT_REPO_URI="https://github.com/fidelram/deepTools"; - KEYWORDS="" -else - SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3" -SLOT="0" -IUSE="" - -DEPEND=">=dev-python/numpy-1.8.0 - >=sci-libs/scipy-0.17.0 - >=dev-python/py2bit-0.1.0 - >=dev-python/pyBigWig-0.2.1 - >=sci-biology/pysam-0.8 - >=dev-python/matplotlib-1.4.0" -RDEPEND="${DEPEND}" - diff --git a/sci-biology/deeptools/deeptools-9999.ebuild b/sci-biology/deeptools/deeptools-9999.ebuild deleted file mode 100644 index 4d6d2fa77..000000000 --- a/sci-biology/deeptools/deeptools-9999.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 python3_5 ) - -inherit distutils-r1 - -[ "$PV" == "9999" ] && inherit git-2 - -DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" -HOMEPAGE="https://github.com/fidelram/deepTools"; -if [ "$PV" == "9999" ]; then - EGIT_REPO_URI="https://github.com/fidelram/deepTools"; - KEYWORDS="" -else - SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3" -SLOT="0" -IUSE="" - -DEPEND=">=dev-python/numpy-1.8.0 - >=sci-libs/scipy-0.17.0 - >=dev-python/py2bit-0.1.0 - >=dev-python/pyBigWig-0.2.1 - >=sci-biology/pysam-0.8 - >=dev-python/matplotlib-1.4.0" -RDEPEND="${DEPEND}" - diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml deleted file mode 100644 index f68a1b6fa..000000000 --- a/sci-biology/deeptools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/mira/mira-4.9.6.ebuild b/sci-biology/mira/mira-4.9.6.ebuild deleted file mode 100644 index 22ddea015..000000000 --- a/sci-biology/mira/mira-4.9.6.ebuild +++ /dev/null @@ -1,93 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - -inherit autotools eutils multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" -HOMEPAGE="http://www.chevreux.org/projects_mira.html"; -SRC_URI=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 -# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -S="${WORKDIR}"/"${PN}"-"${MY_PV}" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) - -# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ - "${FILESDIR}"/${P}-cout.patch \ - "${FILESDIR}"/${P}-DESTDIR.patch - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - eautoreconf -} - -src_configure() { - econf \ - --with-boost="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-thread=boost_thread-mt -} - -#src_compile() { -# base_src_compile -# # TODO: resolve docbook incompatibility for building docs -# if use doc; then emake -C doc clean docs || die; fi -#} - -src_install() { - default - dodoc ${DOCS[@]} - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} - - # if sci-biology/staden is installed, ideally use configprotect? - if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then - if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then - cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die - insinto /usr/share/staden/etc/ - doins "${WORKDIR}"/GTAGDB - fi - fi - if [ -e "/etc/consedrc/" ]; then - insinto /etc/consedrc - doins "${S}"/src/support/consedtaglib.txt - fi -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"; -} diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild index cffdaff97..461e62f84 100644 --- a/sci-biology/plinkseq/plinkseq-9999.ebuild +++ b/sci-biology/plinkseq/plinkseq-9999.ebuild @@ -20,6 +20,7 @@ IUSE="" DEPEND="sys-libs/zlib dev-libs/protobuf + www-servers/mongoose !sci-biology/fsl" # file collision on /usr/bin/mm RDEPEND="${DEPEND}" @@ -28,9 +29,7 @@ src_prepare(){ sed -e "s/= -static/=/g" -i config_defs.Makefile || die rm -rf sources/ext/protobuf-* || die rm sources/ext/protobuf sources/ext/sources/include/google || die - # we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all - # rm -rf sources/mongoose || die - # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die + rm -rf sources/mongoose || die sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die find . -name \*.proto | while read f; do \ d=`dirname $f`; \ @@ -45,13 +44,11 @@ src_prepare(){ sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die local myinc=`pkg-config protobuf --variable=includedir` - sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die + sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile || die local mylib=`pkg-config protobuf --variable=libdir` - sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS - # anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it - sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die + sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die local mylibs=`pkg-config protobuf --libs` - sed -e "[email protected]@ ${mylibs}@ " -i Makefile || die + sed -e "[email protected]@$mylibs@" -i Makefile || die } src_install(){
