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Sat, 10 Jan 2015 14:37:07 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1420899769.1addc38c5ff55f17bdb2da77ecf3463f76463f50.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/pvmsx/ChangeLog sci-biology/pvmsx/metadata.xml sci-biology/pvmsx/pvmsx-0.1.ebuild X-VCS-Directories: sci-biology/pvmsx/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 1addc38c5ff55f17bdb2da77ecf3463f76463f50 X-VCS-Branch: master Date: Sat, 10 Jan 2015 14:37:07 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a6d0c17f-6683-442b-b82a-3b93061dff33 X-Archives-Hash: 0a8229aed0e22b067affd9fa101a940d commit: 1addc38c5ff55f17bdb2da77ecf3463f76463f50 Author: Justin Lecher gentoo org> AuthorDate: Sat Jan 10 14:22:49 2015 +0000 Commit: Justin Lecher gentoo 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 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 @@ - sci-biology - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + 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} }