From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 25F90138A1A for ; Wed, 7 Jan 2015 22:12:35 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B1B2CE0849; Wed, 7 Jan 2015 22:12:33 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 54AAEE0849 for ; Wed, 7 Jan 2015 22:12:33 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 19D843406EE for ; Wed, 7 Jan 2015 22:12:32 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id BC907F166 for ; Wed, 7 Jan 2015 22:12:30 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1420668687.3010ecf4051cb4cbab7d5adfceca5bccf1e312df.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/pvmsx/metadata.xml sci-biology/pvmsx/pvmsx-0.1.ebuild X-VCS-Directories: sci-biology/pvmsx/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 3010ecf4051cb4cbab7d5adfceca5bccf1e312df X-VCS-Branch: master Date: Wed, 7 Jan 2015 22:12:30 +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: da2bb106-743c-4111-a792-e7c564dc7656 X-Archives-Hash: 89582bf1d162496a9b9306d7aa69c9ef commit: 3010ecf4051cb4cbab7d5adfceca5bccf1e312df Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 7 22:11:27 2015 +0000 Commit: Martin Mokrejs fold natur cuni 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 @@ + + + + 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 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} +}