commit: 024e8b388e709b7340cfcb8c620d057fc6bcdef4 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Mar 30 18:25:09 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Mar 30 18:25:09 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=024e8b38
sci-biology/maker: improving the ebuild, needs some perl packages to be first introduced into portage tree; needs proper install and to avoid bundled 3rd-party binaries, not sure if the perl modules are a copy of bioperl or not Package-Manager: portage-2.2.18 sci-biology/maker/ChangeLog | 12 ++++++++ sci-biology/maker/maker-2.31.8.ebuild | 54 +++++++++++++++++++++++++++++++++++ sci-biology/maker/metadata.xml | 9 ++++++ 3 files changed, 75 insertions(+) diff --git a/sci-biology/maker/ChangeLog b/sci-biology/maker/ChangeLog new file mode 100644 index 0000000..d954ed6 --- /dev/null +++ b/sci-biology/maker/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/MAKER +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Sep 2014; Christoph Junghans <ott...@gentoo.org> MAKER-9999.ebuild: + added license + +*MAKER-9999 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +MAKER-9999.ebuild, + +metadata.xml: + a skeleton for a new package diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild new file mode 100644 index 0000000..6bc8ff5 --- /dev/null +++ b/sci-biology/maker/maker-2.31.8.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils perl-module + +DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" +HOMEPAGE="http://www.yandell-lab.org/software/maker.html"; +SRC_URI="maker-"${PV}".tgz" + +RESTRICT="fetch" + +# for academia: GPL-v2 or Artistic-2 +# for commercial: ask +LICENSE="|| ( GPL-2 Artistic-2 )" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm +# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm +DEPEND="virtual/mpi + dev-perl/DBI + dev-perl/DBD-SQLite + dev-perl/File-Which + dev-perl/Bit-Vector + dev-perl/Inline-C + dev-perl/IO-All + dev-perl/libwww-perl + dev-perl/DBD-Pg + virtual/perl-Module-Build + >=sci-biology/bioperl-1.6 + sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) + sci-biology/snap + sci-biology/repeatmasker + sci-biology/exonerate + sci-biology/augustus" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/maker/src + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "maker-"${PV}".tgz and place it into ${DISTDIR}" +} + +src_compile(){ + perl Build.PL || die + ./Build install || die +} diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/maker/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>
