commit: cfc5845ba7d3861c2abb56b3ea564cb432da7b59 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 11 09:14:21 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 11 09:14:21 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cfc5845b
sci-biology/snphylo: new package, needs some R packages and we have to avoid the interactive setup.sh step Package-Manager: portage-2.2.18 sci-biology/snphylo/ChangeLog | 10 +++++++++ sci-biology/snphylo/metadata.xml | 9 ++++++++ sci-biology/snphylo/snphylo-20140701.ebuild | 35 +++++++++++++++++++++++++++++ 3 files changed, 54 insertions(+) diff --git a/sci-biology/snphylo/ChangeLog b/sci-biology/snphylo/ChangeLog new file mode 100644 index 0000000..a04d6e3 --- /dev/null +++ b/sci-biology/snphylo/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/snphylo +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*snphylo-20140701 (11 May 2015) + + 11 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +metadata.xml, + +snphylo-20140701.ebuild: + sci-biology/snphylo: new package, needs some R packages and we have to avoid + the interactive setup.sh step diff --git a/sci-biology/snphylo/metadata.xml b/sci-biology/snphylo/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/snphylo/metadata.xml @@ -0,0 +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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snphylo/snphylo-20140701.ebuild b/sci-biology/snphylo/snphylo-20140701.ebuild new file mode 100644 index 0000000..9734989 --- /dev/null +++ b/sci-biology/snphylo/snphylo-20140701.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Pipeline to generate phylogenetic tree from SNP data" +HOMEPAGE="http://chibba.pgml.uga.edu/snphylo"; +SRC_URI="http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz -> ${P}.tar.gz" +# http://github.com/thlee/SNPhylo +# http://www.biomedcentral.com/1471-2164/15/162 + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/fastdnaml + sci-biology/muscle + sci-biology/phylip" +# http://chibba.pgml.uga.edu/snphylo/install_on_linux.html +# R packages (phangorn, gdsfmt, SNPRelate and getopt) +# $ apt-get -y install r-base-dev r-cran-getopt r-cran-rgl + +S="${WORKDIR}"/"${PN}" + +src_compile(){ + bash setup.sh || die +} + +src_install(){ + dobin snphylo.sh +}
