sci-biology/biopieces: skeleton for a new package; has it's own install.sh script

Package-Manager: portage-2.2.7

5 files changed, 147 insertions, 0 deletions

diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
new file mode 100644
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+++ b/sci-biology/biopieces/ChangeLog
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+# 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/Manifest b/sci-biology/biopieces/Manifest
new file mode 100644
index 000000000..a9f679fc5
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+++ b/sci-biology/biopieces/Manifest
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+DIST biopieces_installer-0.51.sh 13908 SHA256 0a5bec2de370c61de3b05014333c233c5ee1a7f363d3e601ff8968b2cc8a8680 SHA512 6667e48e5035044ea9d5fd9a3f05e61cb73c88acfb936ab58ea14290372ccca5c4c4ceb2ad293d4c4401f343c183071ab10d4d282824178d093427b974617632 WHIRLPOOL 3cfd3aece375c8f374341db6a8332dca496533f8251b2f0bbda95ce78fc64f27a447688b4367d5e9cc53465d46deeff1c7c7cd936eb6d532db4cb1cb862b5f3b
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
new file mode 100644
index 000000000..013596681
--- /dev/null
+++ b/sci-biology/biopieces/biopieces-0.51.ebuild
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+# 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 000000000..013596681
--- /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 000000000..2bc893037
--- /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>