From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/gibbs/Manifest | 1 + sci-biology/gibbs/files/gibbs-demo | 7 ++++++ sci-biology/gibbs/gibbs-3.1.ebuild | 50 ++++++++++++++++++++++++++++++++++++++ sci-biology/gibbs/metadata.xml | 10 ++++++++ 4 files changed, 68 insertions(+) create mode 100644 sci-biology/gibbs/Manifest create mode 100644 sci-biology/gibbs/files/gibbs-demo create mode 100644 sci-biology/gibbs/gibbs-3.1.ebuild create mode 100644 sci-biology/gibbs/metadata.xml (limited to 'sci-biology/gibbs') diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest new file mode 100644 index 00000000000..affcfb9f045 --- /dev/null +++ b/sci-biology/gibbs/Manifest @@ -0,0 +1 @@ +DIST gibbs-3.1.tar.gz 563300 RMD160 063de85a7f1a62bcd63c0838db62cb344ff27abd SHA1 9e6fcddd6036ea0c19259820dcfffa9286cd4e1f SHA256 e8bd62b7d2580b00fc0cdf32ed75ac1ffac29747c75227269a75fd587ba77b69 diff --git a/sci-biology/gibbs/files/gibbs-demo b/sci-biology/gibbs/files/gibbs-demo new file mode 100644 index 00000000000..c58ae3b88e0 --- /dev/null +++ b/sci-biology/gibbs/files/gibbs-demo @@ -0,0 +1,7 @@ +#!/bin/bash + +gibbs /usr/share/gibbs/examples/porins.b185 11 100 -R2000 -s230 +gibbs /usr/share/gibbs/examples/iomps.b58 11 125 -s1 +gibbs /usr/share/gibbs/examples/Igfold.b60x 12,12,12 90,90,90 -s1 +gibbs /usr/share/gibbs/examples/hth90seqs 12 150 -s1 +gibbs /usr/share/gibbs/examples/hth90seqs 18,18,18 20,20,20 -s1 diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild new file mode 100644 index 00000000000..9ed11b43512 --- /dev/null +++ b/sci-biology/gibbs/gibbs-3.1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils multilib + +DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" +HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html" +SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="mpi" +KEYWORDS="amd64 x86" + +DEPEND=" + mpi? ( + virtual/mpi + sys-cluster/mpe2 )" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \ + -e 's/-Werror//' \ + -i configure.in || die + autotools-utils_src_prepare +} + +src_configure() { + if use mpi; then export CC=mpicc; fi + local myeconfargs=( $(use_enable mpi) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + exeinto /usr/$(get_libdir)/${PN} + doexe *.pl + dodoc README ChangeLog +} + +pkg_postinst() { + einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}." + einfo "These scripts require installation of sci-biology/bioperl." +} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml new file mode 100644 index 00000000000..c31e2db7021 --- /dev/null +++ b/sci-biology/gibbs/metadata.xml @@ -0,0 +1,10 @@ + + + + sci-biology + + The Gibbs motif sampler stochastically examines candidate alignments + in an effort to find the best alignment as measured by the maximum + a posteriori (MAP) log-likelihood ratio. + + -- cgit v1.2.1