commit: ae7eb86ca691a1713ac4afef719d7baeb376e45f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 28 14:00:53 2014 +0000 Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com> CommitDate: Mon Mar 31 15:27:34 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae7eb86c
sci-biology/biopieces: skeleton for a new package; has it's own install.sh script Package-Manager: portage-2.2.7 --- sci-biology/biopieces/ChangeLog | 11 +++++ sci-biology/biopieces/biopieces-0.51.ebuild | 63 +++++++++++++++++++++++++++++ sci-biology/biopieces/biopieces-9999.ebuild | 63 +++++++++++++++++++++++++++++ sci-biology/biopieces/metadata.xml | 9 +++++ 4 files changed, 146 insertions(+) diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog new file mode 100644 index 0000000..58b781a --- /dev/null +++ b/sci-biology/biopieces/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/biopieces +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*biopieces-0.51 (28 Mar 2014) +*biopieces-9999 (28 Mar 2014) + + 28 Mar 2014; Martin Mokrejs <[email protected]> + +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml: + sci-biology/biopieces: skeleton for a new package; has it's own install.sh + script diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild new file mode 100644 index 0000000..0135966 --- /dev/null +++ b/sci-biology/biopieces/biopieces-0.51.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit subversion + +DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank" +HOMEPAGE="http://code.google.com/p/biopieces"; +SRC_URI="" +if [ "$PV" == "9999" ]; then + ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"; + KEYWORDS="" +else + SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"; + KEYWORDS="" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="" + +# Ruby terminal-table ? + +DEPEND=">=dev-lang/perl-5.8 + dev-perl/Bit-Vector + dev-perl/SVG + dev-perl/TermReadKey + perl-core/Time-HiRes + dev-perl/DBI + dev-perl/XML-Parser + dev-perl/Carp-Clan + dev-perl/Class-Inspector + dev-perl/HTML-Parser + dev-perl/libwww-perl + dev-perl/SOAP-Lite + dev-perl/URI + dev-perl/Inline + dev-perl/Parse-RecDescent + perl-core/version + perl-core/DB_File + dev-perl/DBD-mysql + >=dev-lang/python-2.6 + dev-lang/ruby + dev-ruby/gnuplot + dev-ruby/narray + dev-ruby/RubyInline" + +# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict +# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict + +RDEPEND="${DEPEND} + sci-biology/ncbi-tools + sci-biology/muscle + sci-biology/mummer + sci-biology/blat + sci-biology/bowtie + sci-biology/bwa + sci-biology/velvet + sci-biology/idba + sci-biology/Ray + sci-biology/scan_for_matches" diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild new file mode 100644 index 0000000..0135966 --- /dev/null +++ b/sci-biology/biopieces/biopieces-9999.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit subversion + +DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank" +HOMEPAGE="http://code.google.com/p/biopieces"; +SRC_URI="" +if [ "$PV" == "9999" ]; then + ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"; + KEYWORDS="" +else + SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"; + KEYWORDS="" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="" + +# Ruby terminal-table ? + +DEPEND=">=dev-lang/perl-5.8 + dev-perl/Bit-Vector + dev-perl/SVG + dev-perl/TermReadKey + perl-core/Time-HiRes + dev-perl/DBI + dev-perl/XML-Parser + dev-perl/Carp-Clan + dev-perl/Class-Inspector + dev-perl/HTML-Parser + dev-perl/libwww-perl + dev-perl/SOAP-Lite + dev-perl/URI + dev-perl/Inline + dev-perl/Parse-RecDescent + perl-core/version + perl-core/DB_File + dev-perl/DBD-mysql + >=dev-lang/python-2.6 + dev-lang/ruby + dev-ruby/gnuplot + dev-ruby/narray + dev-ruby/RubyInline" + +# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict +# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict + +RDEPEND="${DEPEND} + sci-biology/ncbi-tools + sci-biology/muscle + sci-biology/mummer + sci-biology/blat + sci-biology/bowtie + sci-biology/bwa + sci-biology/velvet + sci-biology/idba + sci-biology/Ray + sci-biology/scan_for_matches" diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/biopieces/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>
