From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/
Date: Fri, 28 Mar 2014 14:02:22 +0000 (UTC) [thread overview]
Message-ID: <1396015253.35ad68a597e8b049437e248e0edbd0811fca83cb.mmokrejs@gentoo> (raw)
commit: 35ad68a597e8b049437e248e0edbd0811fca83cb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:00:53 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 14:00:53 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=35ad68a5
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 <mmokrejs@fold.natur.cuni.cz>
+ +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>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
next reply other threads:[~2014-03-28 14:02 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-03-28 14:02 Martin Mokrejs [this message]
-- strict thread matches above, loose matches on Subject: below --
2014-03-31 15:28 [gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/ Nicolas Bock
2014-11-13 13:00 Justin Lecher
2015-02-18 16:41 Justin Lecher
2015-02-18 16:41 Justin Lecher
2015-03-08 18:08 Justin Lecher
2016-06-22 9:37 Martin Mokrejs
2016-09-24 11:26 Martin Mokrejs
2017-09-02 11:55 David Seifert
2020-09-26 9:42 Horea Christian
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