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/reapr/
Date: Wed, 30 Mar 2016 17:20:31
Message-Id: 1459358270.dbff72983c149c6901adfa99351d1e0fa83e7bfe.mmokrejs@gentoo
1 commit: dbff72983c149c6901adfa99351d1e0fa83e7bfe
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Wed Mar 30 17:17:50 2016 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Wed Mar 30 17:17:50 2016 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dbff7298
7
8 sci-biology/reapr: new package with bundled samtools, bamtools, tabix (nowadays part of samtools) and other binaries; does not link probably due to a clash of symbols with my system-wide installed -lbamtools
9
10 Package-Manager: portage-2.2.28
11
12 sci-biology/reapr/metadata.xml | 12 ++++++++
13 sci-biology/reapr/reapr-1.0.18.ebuild | 56 +++++++++++++++++++++++++++++++++++
14 2 files changed, 68 insertions(+)
15
16 diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml
17 new file mode 100644
18 index 0000000..f68a1b6
19 --- /dev/null
20 +++ b/sci-biology/reapr/metadata.xml
21 @@ -0,0 +1,12 @@
22 +<?xml version="1.0" encoding="UTF-8"?>
23 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
24 +<pkgmetadata>
25 + <maintainer type="person">
26 + <email>mmokrejs@×××××××××××××××.cz</email>
27 + <name>Martin Mokrejs</name>
28 + </maintainer>
29 + <maintainer type="project">
30 + <email>sci-biology@g.o</email>
31 + <name>Gentoo Biology Project</name>
32 + </maintainer>
33 +</pkgmetadata>
34
35 diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild
36 new file mode 100644
37 index 0000000..312219a
38 --- /dev/null
39 +++ b/sci-biology/reapr/reapr-1.0.18.ebuild
40 @@ -0,0 +1,56 @@
41 +# Copyright 1999-2016 Gentoo Foundation
42 +# Distributed under the terms of the GNU General Public License v2
43 +# $Id$
44 +
45 +EAPI=5
46 +
47 +DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
48 +HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
49 +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
50 + ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"
51 +
52 +LICENSE="GPL-3"
53 +SLOT="0"
54 +KEYWORDS="" # does not link against -lbamtools
55 +IUSE=""
56 +
57 +# tested smalt versions 0.6.4 to 0.7.0.1 only
58 +DEPEND="sci-biology/bamtools
59 + =sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18
60 +RDEPEND="${DEPEND}"
61 +# sci-biology/smalt
62 +# dev-perl/File-Basename
63 +# dev-perl/File-Copy
64 +# dev-perl/File-Spec
65 +# perl-core/Getopt-Long
66 +# dev-perl/List-Util
67 +# dev-lang/R"
68 +
69 +S="${WORKDIR}"/Reapr_"${PV}"
70 +
71 +src_prepare(){
72 + sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die
73 + sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die
74 + sed -e 's#-O3##' -i src/Makefile || die
75 + sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die
76 + #sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die
77 + sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die
78 + sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die
79 +}
80 +
81 +src_compile(){
82 + cd third_party/tabix || die
83 + emake # to yield tabix.o object
84 + cd ../.. || die
85 + cd src || die
86 + emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a
87 +}
88 +
89 +src_install(){
90 + dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf
91 +}
92 +
93 +pkg_postinst(){
94 + einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"
95 + einfo "You can view results with >=sci-biology/artemis*-15.0.0"
96 +}