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/TransDecoder/, sci-biology/TransDecoder/files/
Date: Wed, 30 Mar 2016 14:50:17
Message-Id: 1459349255.1a200d0a079c95ff7357a3581d1f43be63af802d.mmokrejs@gentoo
1 commit: 1a200d0a079c95ff7357a3581d1f43be63af802d
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Wed Mar 30 14:47:35 2016 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Wed Mar 30 14:47:35 2016 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a200d0a
7
8 sci-biology/TransDecoder: version bump
9
10 Package-Manager: portage-2.2.28
11
12 sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 83 ++++++++++++++++++++++
13 .../files/TransDecoder-2.1.0__fix_paths.patch | 22 ++++++
14 2 files changed, 105 insertions(+)
15
16 diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
17 new file mode 100644
18 index 0000000..9fbcea5
19 --- /dev/null
20 +++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
21 @@ -0,0 +1,83 @@
22 +# Copyright 1999-2016 Gentoo Foundation
23 +# Distributed under the terms of the GNU General Public License v2
24 +# $Id$
25 +
26 +EAPI=5
27 +
28 +[ "$PV" == "9999" ] && inherit git-r3
29 +
30 +PERL_EXPORT_PHASE_FUNCTIONS=no
31 +inherit perl-module eutils toolchain-funcs
32 +
33 +DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
34 +HOMEPAGE="http://transdecoder.github.io"
35 +if [ "$PV" == "9999" ]; then
36 + EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
37 + KEYWORDS=""
38 +else
39 + SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
40 + KEYWORDS="~amd64"
41 + S="${WORKDIR}"/TransDecoder-"${PV}"
42 +fi
43 +
44 +LICENSE="BSD-BroadInstitute"
45 +SLOT="0"
46 +IUSE=""
47 +
48 +DEPEND=""
49 +RDEPEND="${DEPEND}
50 + sci-biology/cd-hit
51 + sci-biology/parafly
52 + sci-biology/ffindex"
53 +
54 +src_prepare(){
55 + rm -rf transdecoder_plugins/cd-hit
56 + for f in PerlLib/*.pm; do
57 + p=`basename $f .pm`;
58 + sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
59 + done
60 + epatch "${FILESDIR}"/"${P}"__fix_paths.patch
61 + epatch "${FILESDIR}"/pfam_runner.pl.patch
62 +}
63 +
64 +src_compile(){
65 + einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
66 +}
67 +
68 +# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
69 +# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
70 +# thread in archives. You can get it from
71 +# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
72 +
73 +src_install(){
74 + dobin TransDecoder.Predict TransDecoder.LongOrfs
75 + insinto /usr/share/${PN}/util
76 + doins util/*.pl
77 + chmod -R a+rx "${D}"/usr/share/${PN}/util
78 + # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
79 + rm -rf util/bin
80 + #
81 + # * sci-biology/trinityrnaseq-20140413:0::science
82 + # * /usr/bin/Fasta_reader.pm
83 + # * /usr/bin/GFF3_utils.pm
84 + # * /usr/bin/Gene_obj.pm
85 + # * /usr/bin/Gene_obj_indexer.pm
86 + # * /usr/bin/Longest_orf.pm
87 + # * /usr/bin/Nuc_translator.pm
88 + # * /usr/bin/TiedHash.pm
89 + #
90 + perl_set_version
91 + insinto ${VENDOR_LIB}/${PN}
92 + doins PerlLib/*.pm
93 + # dodoc Release.Notes
94 + einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
95 + einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
96 + einfo "hmmpress Pfam-A.hmm.bin"
97 +}
98 +
99 +pkg_postinst(){
100 + einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
101 + einfo "at least with NCBI blast from either:"
102 + einfo " sci-biology/ncbi-blast+ (released more often) or from"
103 + einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
104 +}
105
106 diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
107 new file mode 100644
108 index 0000000..0a6fca0
109 --- /dev/null
110 +++ b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
111 @@ -0,0 +1,22 @@
112 +--- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100
113 ++++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100
114 +@@ -64,7 +64,7 @@
115 + use TransDecoder::Fasta_reader;
116 + use TransDecoder::Longest_orf;
117 +
118 +-my $UTIL_DIR = "$FindBin::RealBin/util";
119 ++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
120 + $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
121 +
122 +
123 +--- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100
124 ++++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100
125 +@@ -52,7 +52,7 @@
126 + use TransDecoder::Fasta_reader;
127 + use TransDecoder::Longest_orf;
128 +
129 +-my $UTIL_DIR = "$FindBin::RealBin/util";
130 ++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
131 + $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
132 +
133 +