commit: 3010ecf4051cb4cbab7d5adfceca5bccf1e312df Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 22:11:27 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 22:11:27 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3010ecf4
Initial ebuild --- sci-biology/pvmsx/metadata.xml | 9 ++++++++ sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+) diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/pvmsx/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild new file mode 100644 index 0000000..b194f08 --- /dev/null +++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"; +SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="sys-cluster/pvm" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_unpack(){ + mkdir ${PN} || die + cd ${PN} || die "Failed to chdir" + unpack ${PN}.tar.gz || die +} + +src_prepare() { + # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h + sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" + sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die + sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile + cd ${PN} || die + ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" +} + +src_compile() { + cd ${PN} || die + emake || die "emake failed in "${S}"/${PN}" +} + +src_install() { + cd ${PN} || die + dobin ${PN} || die "Failed to install ${PN} binary" + newdoc README README.${PN} +}
