commit: 61dd48b0c1dc243678bc613f51ab3aedd6e13ba7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Apr 30 22:46:51 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 30 22:46:51 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=61dd48b0
sci-biology/Trinotate: new package Package-Manager: portage-2.2.18 sci-biology/Trinotate/ChangeLog | 9 ++++++ sci-biology/Trinotate/Trinotate-2.0.1.ebuild | 45 ++++++++++++++++++++++++++++ sci-biology/Trinotate/metadata.xml | 9 ++++++ 3 files changed, 63 insertions(+) diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog new file mode 100644 index 0000000..4ef519a --- /dev/null +++ b/sci-biology/Trinotate/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/Trinotate +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Trinotate-2.0.1 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <[email protected]> + +Trinotate-2.0.1.ebuild, +metadata.xml: + sci-biology/Trinotate: new package diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild new file mode 100644 index 0000000..8665fb4 --- /dev/null +++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes" +HOMEPAGE="http://trinotate.github.io"; +SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz"; + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/ncbi-tools++ + sci-biology/trinityrnaseq + sci-biology/TransDecoder" + +# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer +# >=sci-biology/rnammer-2.3.2 +# +# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp +# >=sci-biology/signalp-4 +# +# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm + +# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'. +# In the 'rnammer' software configuration, edit the rnammer script to point +# $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; + +src_install(){ + perl_set_version + dobin Trinotate + insinto /usr/share/"${PN}" + doins -r admin java sample_data util TrinotateWeb + insinto ${VENDOR_LIB}/${PN} + doins -r PerlLib/* + dodoc Release.Notes +} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/Trinotate/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>
