commit: 1addc38c5ff55f17bdb2da77ecf3463f76463f50 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sat Jan 10 14:22:49 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sat Jan 10 14:22:49 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1addc38c
sci-biology/pvmsx: Soma QA and polishing Package-Manager: portage-2.2.15 --- sci-biology/pvmsx/ChangeLog | 7 +++++++ sci-biology/pvmsx/metadata.xml | 10 +++++----- sci-biology/pvmsx/pvmsx-0.1.ebuild | 36 +++++++++++++++++------------------- 3 files changed, 29 insertions(+), 24 deletions(-) diff --git a/sci-biology/pvmsx/ChangeLog b/sci-biology/pvmsx/ChangeLog new file mode 100644 index 0000000..506319d --- /dev/null +++ b/sci-biology/pvmsx/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/pvmsx +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 10 Jan 2015; Justin Lecher <[email protected]> pvmsx-0.1.ebuild, metadata.xml: + Soma QA and polishing + diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml index 07b5255..2bc8930 100644 --- a/sci-biology/pvmsx/metadata.xml +++ b/sci-biology/pvmsx/metadata.xml @@ -1,9 +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> + <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 index b194f08..feac0d2 100644 --- a/sci-biology/pvmsx/pvmsx-0.1.ebuild +++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild @@ -4,43 +4,41 @@ EAPI=5 -DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx" +DESCRIPTION="Parallel multi-FASTA file processing tool" HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"; -SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"; +SRC_URI=" + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${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="${DEPEND}" +#DEPEND="sys-cluster/pvm" +#RDEPEND="${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 ${PN} || die + sed \ + -e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \ + -i "${S}"/Makefile || die "Failed to run sed" + sed \ + -e 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' \ + -i "${S}"/Makefile || die + sed \ + -e "s#-I-#-iquote#" \ + -i "${S}"/Makefile || die ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" } src_compile() { - cd ${PN} || die - emake || die "emake failed in "${S}"/${PN}" + emake } src_install() { - cd ${PN} || die - dobin ${PN} || die "Failed to install ${PN} binary" + dobin ${PN} newdoc README README.${PN} }
