commit: 81a1355ea065924e0c6426772af7c16d90432ccd Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 31 20:51:57 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 31 20:59:27 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=81a1355e
sci-biology/deeptools: add a new package Package-Manager: Portage-2.3.5, Repoman-2.3.1 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, 226 insertions(+), 5 deletions(-) diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/dev-python/pyBigWig/metadata.xml @@ -0,0 +1,12 @@ +<?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 new file mode 100644 index 000000000..33664c388 --- /dev/null +++ b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild @@ -0,0 +1,16 @@ +# 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 new file mode 100644 index 000000000..0e2cd40c8 --- /dev/null +++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild @@ -0,0 +1,18 @@ +# 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="${DEPEND}" diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild new file mode 100644 index 000000000..6f9a41d54 --- /dev/null +++ b/sci-biology/deeptools/deeptools-2.5.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_5 ) + +inherit distutils-r1 + +[ "$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 new file mode 100644 index 000000000..4d6d2fa77 --- /dev/null +++ b/sci-biology/deeptools/deeptools-9999.ebuild @@ -0,0 +1,34 @@ +# 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 new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/deeptools/metadata.xml @@ -0,0 +1,12 @@ +<?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 new file mode 100644 index 000000000..22ddea015 --- /dev/null +++ b/sci-biology/mira/mira-4.9.6.ebuild @@ -0,0 +1,93 @@ +# 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 461e62f84..cffdaff97 100644 --- a/sci-biology/plinkseq/plinkseq-9999.ebuild +++ b/sci-biology/plinkseq/plinkseq-9999.ebuild @@ -20,7 +20,6 @@ IUSE="" DEPEND="sys-libs/zlib dev-libs/protobuf - www-servers/mongoose !sci-biology/fsl" # file collision on /usr/bin/mm RDEPEND="${DEPEND}" @@ -29,7 +28,9 @@ src_prepare(){ sed -e "s/= -static/=/g" -i config_defs.Makefile || die rm -rf sources/ext/protobuf-* || die rm sources/ext/protobuf sources/ext/sources/include/google || die - rm -rf sources/mongoose || die + # we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all + # rm -rf sources/mongoose || die + # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die 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 $f`; \ @@ -44,11 +45,13 @@ src_prepare(){ sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die local myinc=`pkg-config protobuf --variable=includedir` - sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$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)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die + 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 $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it + sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die local mylibs=`pkg-config protobuf --libs` - sed -e "[email protected]@$mylibs@" -i Makefile || die + sed -e "[email protected]@ ${mylibs}@ " -i Makefile || die } src_install(){
