Gentoo Archives: gentoo-commits

From: Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
Date: Sat, 31 Mar 2018 00:15:22
Message-Id: 1522455301.3724acdd4d192ac400d81a94f91e957c0e832ccd.mmokrejs@gentoo
1 commit: 3724acdd4d192ac400d81a94f91e957c0e832ccd
2 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Sat Mar 31 00:15:01 2018 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Sat Mar 31 00:15:01 2018 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3724acdd
7
8 sci-biology/BRAKER: version bump, update LICENSE
9
10 Package-Manager: Portage-2.3.24, Repoman-2.3.6
11
12 .../{BRAKER-2.ebuild => BRAKER-2.1.0.ebuild} | 30 +++++++++-------------
13 1 file changed, 12 insertions(+), 18 deletions(-)
14
15 diff --git a/sci-biology/BRAKER/BRAKER-2.ebuild b/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
16 similarity index 58%
17 rename from sci-biology/BRAKER/BRAKER-2.ebuild
18 rename to sci-biology/BRAKER/BRAKER-2.1.0.ebuild
19 index b4c752457..13d63d4b8 100644
20 --- a/sci-biology/BRAKER/BRAKER-2.ebuild
21 +++ b/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
22 @@ -10,15 +10,17 @@ DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
23 # http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
24 HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
25 http://bioinf.uni-greifswald.de/augustus/downloads"
26 -SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER"${PV}".tar.gz -> ${P}.tar.gz"
27 -# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
28 -# The most recent release is version 1.8, from December 15th 2015.
29 -# Example data for testing the BRAKER1 pipeline is available at
30 -# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1examples.tar.gz (1.1 GB).
31 -
32 -LICENSE="GPL-3"
33 +SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${PV}".tar.gz -> ${P}.tar.gz"
34 +# Example data for testing the BRAKER2 pipeline is available at
35 +# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz (1.1 GB).
36 +
37 +# BRAKER2 is using the Artistic-1.0 version without clause 8 about
38 +# commercial distribution
39 +# See discussion at https://opensource.org/licenses/artistic-license-1.0
40 +# Practically the license is same as http://dev.perl.org/licenses/artistic.html
41 +LICENSE="Artistic"
42 SLOT="0"
43 -KEYWORDS=""
44 +KEYWORDS="~amd64 ~x86"
45 IUSE=""
46
47 DEPEND=""
48 @@ -26,23 +28,15 @@ RDEPEND="${DEPEND}
49 dev-perl/Scalar-Util-Numeric
50 sci-biology/augustus"
51 #>=sci-biology/GeneMark_ET-bin-4.29"
52 -#
53 -# BUG:
54 -# this causes:
55 -# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
56 -
57 -S="${WORKDIR}"/BRAKER_v"${PV}".0
58
59 -src_prepare(){
60 - sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
61 -}
62 +S="${WORKDIR}"/BRAKER_v"${PV}"
63
64 src_install(){
65 perl_set_version
66 dobin *.pl
67 insinto ${VENDOR_LIB}/${PN}
68 doins *.pm
69 - dodoc README.braker
70 + dodoc userguide.pdf
71 }
72
73 pkg_postinst(){