diff options
Diffstat (limited to 'sci-biology/samtools')
| -rw-r--r-- | sci-biology/samtools/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.12.ebuild | 7 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.12a-r1.ebuild | 4 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.16.ebuild | 41 |
4 files changed, 52 insertions, 8 deletions
diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog index 8ac0f6446300..99a1483e3bfc 100644 --- a/sci-biology/samtools/ChangeLog +++ b/sci-biology/samtools/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/samtools # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.5 2011/03/14 09:37:27 xarthisius Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.6 2011/04/30 11:12:49 jlec Exp $ + +*samtools-0.1.16 (30 Apr 2011) + + 30 Apr 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild, + samtools-0.1.12a-r1.ebuild, +samtools-0.1.16.ebuild: + Version BUmp, #365265 *samtools-0.1.12a-r1 (14 Mar 2011) diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild index a2953ebbd51c..bd221c67fb5f 100644 --- a/sci-biology/samtools/samtools-0.1.12.ebuild +++ b/sci-biology/samtools/samtools-0.1.12.ebuild @@ -1,13 +1,13 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.3 2011/02/17 09:05:13 tomka Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.4 2011/04/30 11:12:50 jlec Exp $ EAPI="2" MY_P="${P}a" DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" -HOMEPAGE="http://${PN}.sourceforge.net/" +HOMEPAGE="http://samtools.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2" LICENSE="MIT" @@ -15,9 +15,6 @@ SLOT="0" IUSE="" KEYWORDS="amd64 x86" -DEPEND="" -RDEPEND="" - S="${WORKDIR}/${MY_P}" src_prepare() { diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild index 963f27c77d57..8f9f30d2e6df 100644 --- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild +++ b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.1 2011/03/14 09:37:27 xarthisius Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.2 2011/04/30 11:12:49 jlec Exp $ EAPI="2" @@ -33,7 +33,7 @@ src_install() { dobin $(find misc -type f -executable) || die dolib.so libbam.so.1 || die insinto /usr/include/bam - doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h|| die + doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die insinto /usr/share/${PN} doins -r examples || die doman ${PN}.1 || die diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild new file mode 100644 index 000000000000..949d0f92aa9d --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.16.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.1 2011/04/30 11:12:50 jlec Exp $ + +EAPI="2" + +inherit toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +src_prepare() { + sed -e '/^CFLAGS=/d' \ + -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ + -e "s/-shared/& \$(LDFLAGS)/" \ + -i "${S}"/{Makefile,misc/Makefile} || die #358563 + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die +} + +src_compile() { + emake CC="$(tc-getCC)" dylib || die + emake CC="$(tc-getCC)" || die +} + +src_install() { + dobin samtools || die + dobin $(find misc -type f -executable) || die + dolib.so libbam.so.1 || die + insinto /usr/include/bam + doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die + insinto /usr/share/${PN} + doins -r examples || die + doman ${PN}.1 || die + dodoc AUTHORS ChangeLog NEWS +} |