commit: dc8f115ece85ad0ba1cae058febbb79ee40b89c1 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 10 21:04:10 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 10 21:04:10 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc8f115e
sci-biology/oases: new package Package-Manager: portage-2.2.28 sci-biology/oases/files/Makefile.patch | 15 +++++++++++++ sci-biology/oases/metadata.xml | 12 +++++++++++ sci-biology/oases/oases-0.2.08.ebuild | 34 +++++++++++++++++++++++++++++ sci-biology/oases/oases-9999.ebuild | 39 ++++++++++++++++++++++++++++++++++ 4 files changed, 100 insertions(+) diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch new file mode 100644 index 0000000..58652b0 --- /dev/null +++ b/sci-biology/oases/files/Makefile.patch @@ -0,0 +1,15 @@ +--- Makefile.ori 2016-04-10 22:34:31.976222662 +0200 ++++ Makefile 2016-04-10 22:37:49.636225327 +0200 +@@ -1,8 +1,8 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g ++CC ?= gcc ++CFLAGS ?= -Wall ++DEBUG ?= -g + LIBS = -lm +-OPT = -O3 ++#OPT = -O3 + export MAXKMERLENGTH = 64 + export CATEGORIES = 2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/oases/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild new file mode 100644 index 0000000..eff7842 --- /dev/null +++ b/sci-biology/oases/oases-0.2.08.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="De novo transcriptome assembler" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"; +SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz + http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"; +KEYWORDS="" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=sci-biology/velvet-1.2.08" + +S="${WORKDIR}"/oases_0.2.8 + +src_prepare(){ + epatch "${FILESDIR}"/Makefile.patch + sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die +} + +src_install(){ + dobin oases + dodoc README.md + dodoc "${DISTDIR}"/OasesManual.pdf +} diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild new file mode 100644 index 0000000..0c54394 --- /dev/null +++ b/sci-biology/oases/oases-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-r3 + +inherit eutils + +DESCRIPTION="De novo transcriptome assembler" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"; +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="git://github.com/dzerbino/oases.git" + SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"; + KEYWORDS="" +else + SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz + http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"; + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=sci-biology/velvet-1.2.08" + +src_prepare(){ + epatch "${FILESDIR}"/Makefile.patch +} + +src_install(){ + dobin oases + dodoc README.md + dodoc "${DISTDIR}"/OasesManual.pdf +}
