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jlec 13/03/29 17:29:49 |
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Modified: ChangeLog |
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Added: samtools-0.1.18-r3.ebuild |
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Log: |
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sci-biology/samtools: Install bcftools and vcfutils.pl pointed out by mahnmut |
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(Portage version: 2.2.0_alpha169/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) |
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Revision Changes Path |
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1.12 sci-biology/samtools/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.12&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.12&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?r1=1.11&r2=1.12 |
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v |
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retrieving revision 1.11 |
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retrieving revision 1.12 |
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diff -u -r1.11 -r1.12 |
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--- ChangeLog 11 Mar 2013 16:56:12 -0000 1.11 |
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+++ ChangeLog 29 Mar 2013 17:29:49 -0000 1.12 |
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@@ -1,6 +1,11 @@ |
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# ChangeLog for sci-biology/samtools |
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# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.11 2013/03/11 16:56:12 jlec Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.12 2013/03/29 17:29:49 jlec Exp $ |
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+ |
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+*samtools-0.1.18-r3 (29 Mar 2013) |
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+ |
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+ 29 Mar 2013; Justin Lecher <jlec@g.o> +samtools-0.1.18-r3.ebuild: |
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+ Install bcftools and vcfutils.pl pointed out by mahnmut |
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11 Mar 2013; Justin Lecher <jlec@g.o> metadata.xml: |
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Drop Andrey as maintainer so that bugs get assigned to sci-biology directly |
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1.1 sci-biology/samtools/samtools-0.1.18-r3.ebuild |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r3.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r3.ebuild?rev=1.1&content-type=text/plain |
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Index: samtools-0.1.18-r3.ebuild |
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=================================================================== |
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# Copyright 1999-2013 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r3.ebuild,v 1.1 2013/03/29 17:29:49 jlec Exp $ |
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EAPI=5 |
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inherit multilib toolchain-funcs |
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DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" |
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HOMEPAGE="http://samtools.sourceforge.net/" |
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SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" |
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|
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LICENSE="MIT" |
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SLOT="0" |
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IUSE="examples" |
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KEYWORDS="~amd64 ~x86 ~x64-macos" |
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RDEPEND="sys-libs/ncurses" |
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DEPEND="${RDEPEND} |
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virtual/pkgconfig" |
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src_prepare() { |
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sed \ |
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-e '/^CC/s:=:?=:g' \ |
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-e "/^LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \ |
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-e '/^CFLAGS=/s:=:?=:' \ |
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-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ |
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-e "s/-shared/& \$(LDFLAGS)/" \ |
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-i "${S}"/{bcftools,misc,}/Makefile || die #358563 |
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sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die |
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tc-export CC |
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} |
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src_compile() { |
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emake dylib |
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emake |
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} |
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src_install() { |
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dobin samtools $(find bcftools misc -type f -executable) |
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dolib.so libbam.so.1 |
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dosym libbam.so.1 /usr/$(get_libdir)/libbam.so |
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insinto /usr/include/bam |
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doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h |
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doman ${PN}.1 |
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dodoc AUTHORS ChangeLog NEWS |
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|
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if use examples; then |
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insinto /usr/share/${PN} |
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doins -r examples |
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fi |
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} |
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