| 1 |
jlec 13/12/06 12:48:36 |
| 2 |
|
| 3 |
Modified: ChangeLog |
| 4 |
Added: samtools-0.1.19-r1.ebuild |
| 5 |
Removed: samtools-0.1.19.ebuild |
| 6 |
Log: |
| 7 |
sci-biology/samtools: Fix underlinking |
| 8 |
|
| 9 |
(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
| 10 |
|
| 11 |
Revision Changes Path |
| 12 |
1.15 sci-biology/samtools/ChangeLog |
| 13 |
|
| 14 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.15&view=markup |
| 15 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.15&content-type=text/plain |
| 16 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?r1=1.14&r2=1.15 |
| 17 |
|
| 18 |
Index: ChangeLog |
| 19 |
=================================================================== |
| 20 |
RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v |
| 21 |
retrieving revision 1.14 |
| 22 |
retrieving revision 1.15 |
| 23 |
diff -u -r1.14 -r1.15 |
| 24 |
--- ChangeLog 6 Dec 2013 12:44:16 -0000 1.14 |
| 25 |
+++ ChangeLog 6 Dec 2013 12:48:36 -0000 1.15 |
| 26 |
@@ -1,6 +1,12 @@ |
| 27 |
# ChangeLog for sci-biology/samtools |
| 28 |
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
| 29 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.14 2013/12/06 12:44:16 jlec Exp $ |
| 30 |
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.15 2013/12/06 12:48:36 jlec Exp $ |
| 31 |
+ |
| 32 |
+*samtools-0.1.19-r1 (06 Dec 2013) |
| 33 |
+ |
| 34 |
+ 06 Dec 2013; Justin Lecher <jlec@g.o> -samtools-0.1.19.ebuild, |
| 35 |
+ +samtools-0.1.19-r1.ebuild, files/samtools-0.1.19-buildsystem.patch: |
| 36 |
+ Fix underlinking |
| 37 |
|
| 38 |
06 Dec 2013; Justin Lecher <jlec@g.o> samtools-0.1.12.ebuild, |
| 39 |
samtools-0.1.18.ebuild, samtools-0.1.18-r2.ebuild, samtools-0.1.18-r3.ebuild, |
| 40 |
|
| 41 |
|
| 42 |
|
| 43 |
1.1 sci-biology/samtools/samtools-0.1.19-r1.ebuild |
| 44 |
|
| 45 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r1.ebuild?rev=1.1&view=markup |
| 46 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r1.ebuild?rev=1.1&content-type=text/plain |
| 47 |
|
| 48 |
Index: samtools-0.1.19-r1.ebuild |
| 49 |
=================================================================== |
| 50 |
# Copyright 1999-2013 Gentoo Foundation |
| 51 |
# Distributed under the terms of the GNU General Public License v2 |
| 52 |
# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r1.ebuild,v 1.1 2013/12/06 12:48:36 jlec Exp $ |
| 53 |
|
| 54 |
EAPI=5 |
| 55 |
|
| 56 |
PYTHON_COMPAT=( python{2_6,2_7} ) |
| 57 |
|
| 58 |
inherit eutils multilib python-r1 toolchain-funcs |
| 59 |
|
| 60 |
DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" |
| 61 |
HOMEPAGE="http://samtools.sourceforge.net/" |
| 62 |
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
| 63 |
|
| 64 |
LICENSE="MIT" |
| 65 |
SLOT="0" |
| 66 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" |
| 67 |
IUSE="examples" |
| 68 |
|
| 69 |
REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| 70 |
|
| 71 |
CDEPEND="sys-libs/ncurses" |
| 72 |
RDEPEND="${CDEPEND} |
| 73 |
dev-lang/lua |
| 74 |
dev-lang/perl" |
| 75 |
DEPEND="${CDEPEND} |
| 76 |
virtual/pkgconfig" |
| 77 |
|
| 78 |
src_prepare() { |
| 79 |
epatch "${FILESDIR}"/${P}-buildsystem.patch |
| 80 |
|
| 81 |
sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
| 82 |
|
| 83 |
tc-export CC AR |
| 84 |
} |
| 85 |
|
| 86 |
src_compile() { |
| 87 |
local _ncurses="$(pkg-config --libs ncurses)" |
| 88 |
emake dylib LIBCURSES="${_ncurses}" |
| 89 |
emake LIBCURSES="${_ncurses}" |
| 90 |
} |
| 91 |
|
| 92 |
src_install() { |
| 93 |
dobin samtools $(find bcftools misc -type f -executable) |
| 94 |
|
| 95 |
python_replicate_script "${ED}"/usr/bin/varfilter.py |
| 96 |
|
| 97 |
dolib.so libbam.so.1 |
| 98 |
dosym libbam.so.1 /usr/$(get_libdir)/libbam.so |
| 99 |
|
| 100 |
insinto /usr/include/bam |
| 101 |
doins *.h |
| 102 |
|
| 103 |
doman ${PN}.1 |
| 104 |
dodoc AUTHORS NEWS |
| 105 |
|
| 106 |
if use examples; then |
| 107 |
insinto /usr/share/${PN} |
| 108 |
doins -r examples |
| 109 |
fi |
| 110 |
} |
Archives