commit: 7d88d8fde0145c729b2cf3f147370866db7ed14c Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jan 8 22:31:12 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jan 8 22:31:12 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d88d8fd
sci-biology/transdecoder: new package Package-Manager: portage-2.2.7 --- sci-biology/transdecoder/ChangeLog | 9 +++++ sci-biology/transdecoder/metadata.xml | 9 +++++ .../transdecoder/transdecoder-20140704.ebuild | 44 ++++++++++++++++++++++ 3 files changed, 62 insertions(+) diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog new file mode 100644 index 0000000..252ef53 --- /dev/null +++ b/sci-biology/transdecoder/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/transdecoder +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*transdecoder-20140704 (08 Jan 2015) + + 08 Jan 2015; Martin Mokrejs <[email protected]> +metadata.xml, + +transdecoder-20140704.ebuild: + sci-biology/transdecoder: new package diff --git a/sci-biology/transdecoder/metadata.xml b/sci-biology/transdecoder/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/transdecoder/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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild new file mode 100644 index 0000000..c539231 --- /dev/null +++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit perl-module + +DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" +HOMEPAGE="http://sourceforge.net/projects/transdecoder/"; +SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"; + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sys-cluster/openmpi + sci-biology/hmmer + sci-biology/cd-hit + sci-biology/parafly + sci-biology/ffindex" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/TransDecoder_r20140704 + +src_prepare(){ + rm -rf 3rd_party + mv Makefile Makefile.old +} + +# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see +# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives +# +# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin + +src_install(){ + dobin TransDecoder *.pl util/*.pl util/*.sh + eval `perl '-V:installvendorlib'` + vendor_lib_install_dir="${installvendorlib}" + dodir ${vendor_lib_install_dir} + insinto ${vendor_lib_install_dir} + doins PerlLib/*.pm +}
