From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id DB1D11387FD for ; Mon, 31 Mar 2014 15:28:51 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 3DE38E0A00; Mon, 31 Mar 2014 15:28:41 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 73A97E0A00 for ; Mon, 31 Mar 2014 15:28:40 +0000 (UTC) Received: from spoonbill.gentoo.org (spoonbill.gentoo.org [81.93.255.5]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C3FBA33FBD4 for ; Mon, 31 Mar 2014 15:28:38 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by spoonbill.gentoo.org (Postfix) with ESMTP id 570BE188F8 for ; Mon, 31 Mar 2014 15:28:36 +0000 (UTC) From: "Nicolas Bock" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Nicolas Bock" Message-ID: <1396279654.ae7eb86ca691a1713ac4afef719d7baeb376e45f.nicolasbock@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/biopieces/ChangeLog sci-biology/biopieces/biopieces-0.51.ebuild sci-biology/biopieces/biopieces-9999.ebuild sci-biology/biopieces/metadata.xml X-VCS-Directories: sci-biology/biopieces/ X-VCS-Committer: nicolasbock X-VCS-Committer-Name: Nicolas Bock X-VCS-Revision: ae7eb86ca691a1713ac4afef719d7baeb376e45f X-VCS-Branch: master Date: Mon, 31 Mar 2014 15:28:36 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 88966cf1-0512-4ffa-b6fe-d15963b64800 X-Archives-Hash: 55514bc7f892b89d57e048db8767a7bd commit: ae7eb86ca691a1713ac4afef719d7baeb376e45f Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Fri Mar 28 14:00:53 2014 +0000 Commit: Nicolas Bock gmail 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 + +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 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +