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 }