Gentoo Archives: gentoo-commits

From: Nicolas Bock <nicolasbock@×××××.com>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopieces/
Date: Mon, 31 Mar 2014 15:28:51
Message-Id: 1396279654.ae7eb86ca691a1713ac4afef719d7baeb376e45f.nicolasbock@gentoo
1 commit: ae7eb86ca691a1713ac4afef719d7baeb376e45f
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Fri Mar 28 14:00:53 2014 +0000
4 Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
5 CommitDate: Mon Mar 31 15:27:34 2014 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae7eb86c
7
8 sci-biology/biopieces: skeleton for a new package; has it's own install.sh script
9
10 Package-Manager: portage-2.2.7
11
12 ---
13 sci-biology/biopieces/ChangeLog | 11 +++++
14 sci-biology/biopieces/biopieces-0.51.ebuild | 63 +++++++++++++++++++++++++++++
15 sci-biology/biopieces/biopieces-9999.ebuild | 63 +++++++++++++++++++++++++++++
16 sci-biology/biopieces/metadata.xml | 9 +++++
17 4 files changed, 146 insertions(+)
18
19 diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog
20 new file mode 100644
21 index 0000000..58b781a
22 --- /dev/null
23 +++ b/sci-biology/biopieces/ChangeLog
24 @@ -0,0 +1,11 @@
25 +# ChangeLog for sci-biology/biopieces
26 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
27 +# $Header: $
28 +
29 +*biopieces-0.51 (28 Mar 2014)
30 +*biopieces-9999 (28 Mar 2014)
31 +
32 + 28 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
33 + +biopieces-0.51.ebuild, +biopieces-9999.ebuild, +metadata.xml:
34 + sci-biology/biopieces: skeleton for a new package; has it's own install.sh
35 + script
36
37 diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
38 new file mode 100644
39 index 0000000..0135966
40 --- /dev/null
41 +++ b/sci-biology/biopieces/biopieces-0.51.ebuild
42 @@ -0,0 +1,63 @@
43 +# Copyright 1999-2014 Gentoo Foundation
44 +# Distributed under the terms of the GNU General Public License v2
45 +# $Header: $
46 +
47 +EAPI=5
48 +
49 +[ "$PV" == "9999" ] && inherit subversion
50 +
51 +DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
52 +HOMEPAGE="http://code.google.com/p/biopieces"
53 +SRC_URI=""
54 +if [ "$PV" == "9999" ]; then
55 + ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
56 + KEYWORDS=""
57 +else
58 + SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
59 + KEYWORDS=""
60 +fi
61 +
62 +LICENSE="GPL-2"
63 +SLOT="0"
64 +IUSE=""
65 +
66 +# Ruby terminal-table ?
67 +
68 +DEPEND=">=dev-lang/perl-5.8
69 + dev-perl/Bit-Vector
70 + dev-perl/SVG
71 + dev-perl/TermReadKey
72 + perl-core/Time-HiRes
73 + dev-perl/DBI
74 + dev-perl/XML-Parser
75 + dev-perl/Carp-Clan
76 + dev-perl/Class-Inspector
77 + dev-perl/HTML-Parser
78 + dev-perl/libwww-perl
79 + dev-perl/SOAP-Lite
80 + dev-perl/URI
81 + dev-perl/Inline
82 + dev-perl/Parse-RecDescent
83 + perl-core/version
84 + perl-core/DB_File
85 + dev-perl/DBD-mysql
86 + >=dev-lang/python-2.6
87 + dev-lang/ruby
88 + dev-ruby/gnuplot
89 + dev-ruby/narray
90 + dev-ruby/RubyInline"
91 +
92 +# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
93 +# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
94 +
95 +RDEPEND="${DEPEND}
96 + sci-biology/ncbi-tools
97 + sci-biology/muscle
98 + sci-biology/mummer
99 + sci-biology/blat
100 + sci-biology/bowtie
101 + sci-biology/bwa
102 + sci-biology/velvet
103 + sci-biology/idba
104 + sci-biology/Ray
105 + sci-biology/scan_for_matches"
106
107 diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
108 new file mode 100644
109 index 0000000..0135966
110 --- /dev/null
111 +++ b/sci-biology/biopieces/biopieces-9999.ebuild
112 @@ -0,0 +1,63 @@
113 +# Copyright 1999-2014 Gentoo Foundation
114 +# Distributed under the terms of the GNU General Public License v2
115 +# $Header: $
116 +
117 +EAPI=5
118 +
119 +[ "$PV" == "9999" ] && inherit subversion
120 +
121 +DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
122 +HOMEPAGE="http://code.google.com/p/biopieces"
123 +SRC_URI=""
124 +if [ "$PV" == "9999" ]; then
125 + ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
126 + KEYWORDS=""
127 +else
128 + SRC_URI="http://biopieces.googlecode.com/files/biopieces_installer-"${PV}".sh"
129 + KEYWORDS=""
130 +fi
131 +
132 +LICENSE="GPL-2"
133 +SLOT="0"
134 +IUSE=""
135 +
136 +# Ruby terminal-table ?
137 +
138 +DEPEND=">=dev-lang/perl-5.8
139 + dev-perl/Bit-Vector
140 + dev-perl/SVG
141 + dev-perl/TermReadKey
142 + perl-core/Time-HiRes
143 + dev-perl/DBI
144 + dev-perl/XML-Parser
145 + dev-perl/Carp-Clan
146 + dev-perl/Class-Inspector
147 + dev-perl/HTML-Parser
148 + dev-perl/libwww-perl
149 + dev-perl/SOAP-Lite
150 + dev-perl/URI
151 + dev-perl/Inline
152 + dev-perl/Parse-RecDescent
153 + perl-core/version
154 + perl-core/DB_File
155 + dev-perl/DBD-mysql
156 + >=dev-lang/python-2.6
157 + dev-lang/ruby
158 + dev-ruby/gnuplot
159 + dev-ruby/narray
160 + dev-ruby/RubyInline"
161 +
162 +# sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict
163 +# sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict
164 +
165 +RDEPEND="${DEPEND}
166 + sci-biology/ncbi-tools
167 + sci-biology/muscle
168 + sci-biology/mummer
169 + sci-biology/blat
170 + sci-biology/bowtie
171 + sci-biology/bwa
172 + sci-biology/velvet
173 + sci-biology/idba
174 + sci-biology/Ray
175 + sci-biology/scan_for_matches"
176
177 diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
178 new file mode 100644
179 index 0000000..2bc8930
180 --- /dev/null
181 +++ b/sci-biology/biopieces/metadata.xml
182 @@ -0,0 +1,9 @@
183 +<?xml version="1.0" encoding="UTF-8"?>
184 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
185 +<pkgmetadata>
186 + <herd>sci-biology</herd>
187 + <maintainer>
188 + <email>mmokrejs@×××××××××××××××.cz</email>
189 + <name>Martin Mokrejs</name>
190 + </maintainer>
191 +</pkgmetadata>