diff options
Diffstat (limited to 'sci-biology/gibbs')
| -rw-r--r-- | sci-biology/gibbs/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/gibbs/files/gibbs-demo | 7 | ||||
| -rw-r--r-- | sci-biology/gibbs/gibbs-3.1.ebuild | 50 | ||||
| -rw-r--r-- | sci-biology/gibbs/metadata.xml | 10 |
4 files changed, 68 insertions, 0 deletions
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest new file mode 100644 index 000000000000..affcfb9f045f --- /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 000000000000..c58ae3b88e04 --- /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 000000000000..9ed11b435129 --- /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 000000000000..c31e2db70216 --- /dev/null +++ b/sci-biology/gibbs/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + 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. + </longdescription> +</pkgmetadata> |