[gentoo-commits] gentoo-x86 commit in sci-biology/samtools: ChangeLog samtools-0.1.19-r2.ebuild samtools-1.0.ebuild samtools-0.1.18-r2.ebuild samtools-0.1.18-r3.ebuild samtools-0.1.18.ebuild

[Justin Lecher (jlec)]

jlec        14/09/20 19:39:21

  Modified:             ChangeLog samtools-0.1.19-r2.ebuild
  Added:                samtools-1.0.ebuild
  Removed:              samtools-0.1.18-r2.ebuild samtools-0.1.18-r3.ebuild
                        samtools-0.1.18.ebuild
  Log:
  sci-biology/samtools: Version Bump, #523224; drop old
  
  (Portage version: 2.2.13/cvs/Linux x86_64, signed Manifest commit with key 
B9D4F231BD1558AB!)

Revision  Changes    Path
1.18                 sci-biology/samtools/ChangeLog

file : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.18&view=markup
plain: 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.18&content-type=text/plain
diff : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?r1=1.17&r2=1.18

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- ChangeLog   23 Mar 2014 15:29:13 -0000      1.17
+++ ChangeLog   20 Sep 2014 19:39:21 -0000      1.18
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/samtools
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.17 
2014/03/23 15:29:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.18 
2014/09/20 19:39:21 jlec Exp $
+
+*samtools-1.0 (20 Sep 2014)
+
+  20 Sep 2014; Justin Lecher <j...@gentoo.org> -samtools-0.1.18.ebuild,
+  -samtools-0.1.18-r2.ebuild, -samtools-0.1.18-r3.ebuild,
+  samtools-0.1.19-r2.ebuild, +samtools-1.0.ebuild:
+  Version Bump, #523224; drop old
 
 *samtools-0.1.19-r2 (23 Mar 2014)
 



1.2                  sci-biology/samtools/samtools-0.1.19-r2.ebuild

file : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild?rev=1.2&view=markup
plain: 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild?rev=1.2&content-type=text/plain
diff : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild?r1=1.1&r2=1.2

Index: samtools-0.1.19-r2.ebuild
===================================================================
RCS file: 
/var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- samtools-0.1.19-r2.ebuild   23 Mar 2014 15:29:13 -0000      1.1
+++ samtools-0.1.19-r2.ebuild   20 Sep 2014 19:39:21 -0000      1.2
@@ -1,6 +1,6 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: 
/var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild,v 1.1 
2014/03/23 15:29:13 jlec Exp $
+# $Header: 
/var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.19-r2.ebuild,v 1.2 
2014/09/20 19:39:21 jlec Exp $
 
 EAPI=5
 
@@ -35,7 +35,7 @@
 }
 
 src_compile() {
-       local _ncurses="$(pkg-config --libs ncurses)"
+       local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
        emake dylib LIBCURSES="${_ncurses}"
        emake LIBCURSES="${_ncurses}"
 }



1.1                  sci-biology/samtools/samtools-1.0.ebuild

file : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-1.0.ebuild?rev=1.1&view=markup
plain: 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-1.0.ebuild?rev=1.1&content-type=text/plain

Index: samtools-1.0.ebuild
===================================================================
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.0.ebuild,v 
1.1 2014/09/20 19:39:21 jlec Exp $

EAPI=5

PYTHON_COMPAT=( python2_7 )

inherit eutils multilib python-r1 toolchain-funcs

DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large 
nucleotide sequence alignments"
HOMEPAGE="http://www.htslib.org/";
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"

LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
IUSE="examples"

REQUIRED_USE="${PYTHON_REQUIRED_USE}"

CDEPEND="sys-libs/ncurses"

RDEPEND="${CDEPEND}
        dev-lang/lua
        dev-lang/perl
        sci-libs/htslib"
DEPEND="${CDEPEND}
        virtual/pkgconfig"

src_prepare() {
        find htslib-1.0 -delete || die

        sed -i 's~/software/bin/python~/usr/bin/env python~' 
"${S}"/misc/varfilter.py || die

        tc-export CC AR

        sed \
                -e '/htslib.mk/d' \
                -i Makefile || die

}

src_compile() {
        local mymakeargs=(
                LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
                CC="$(tc-getCC)"
                LDFLAGS="${LDFLAGS}"
                CFLAGS="${CFLAGS}"
                HTSDIR="${EPREFIX}/usr/include"
                HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
                )
        emake "${mymakeargs[@]}"
}

src_install() {
        dobin samtools $(find misc -type f -executable)

        python_replicate_script "${ED}"/usr/bin/varfilter.py

        doman ${PN}.1
        dodoc AUTHORS NEWS README

        if use examples; then
                insinto /usr/share/${PN}
                doins -r examples
        fi
}