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 | 4 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.12a-r1.ebuild | 20 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.16.ebuild | 20 | ||||
| -rw-r--r-- | sci-biology/samtools/samtools-0.1.17.ebuild | 48 |
5 files changed, 83 insertions, 17 deletions
diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog index 99a1483e3bfc..99890c78a18f 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 1.6 2011/04/30 11:12:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.7 2011/07/18 01:50:51 jlec Exp $ + +*samtools-0.1.17 (18 Jul 2011) + + 18 Jul 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild, + samtools-0.1.12a-r1.ebuild, samtools-0.1.16.ebuild, +samtools-0.1.17.ebuild: + Version Bump, #375519 *samtools-0.1.16 (30 Apr 2011) diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild index bd221c67fb5f..9cdeed8532b5 100644 --- a/sci-biology/samtools/samtools-0.1.12.ebuild +++ b/sci-biology/samtools/samtools-0.1.12.ebuild @@ -1,8 +1,8 @@ # 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 1.4 2011/04/30 11:12:50 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.5 2011/07/18 01:50:51 jlec Exp $ -EAPI="2" +EAPI=2 MY_P="${P}a" diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild index 8f9f30d2e6df..5c689a266cee 100644 --- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild +++ b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild @@ -1,10 +1,10 @@ # 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 1.2 2011/04/30 11:12:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.3 2011/07/18 01:50:51 jlec Exp $ -EAPI="2" +EAPI=2 -inherit toolchain-funcs +inherit toolchain-funcs multilib DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" HOMEPAGE="http://samtools.sourceforge.net/" @@ -12,11 +12,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" LICENSE="MIT" SLOT="0" -IUSE="" +IUSE="examples" KEYWORDS="~amd64 ~x86 ~x64-macos" src_prepare() { - sed -e '/^CFLAGS=/d' \ + sed \ + -e '/^CFLAGS=/d' \ -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ -e "s/-shared/& \$(LDFLAGS)/" \ -i "${S}"/{Makefile,misc/Makefile} || die #358563 @@ -32,10 +33,15 @@ src_install() { dobin samtools || die dobin $(find misc -type f -executable) || die dolib.so libbam.so.1 || die + dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || 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 ${PN}.1 || die dodoc AUTHORS ChangeLog NEWS + + if use examples; then + insinto /usr/share/${PN} + doins -r examples || die + fi } diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild index 949d0f92aa9d..a2181d1f6cfc 100644 --- a/sci-biology/samtools/samtools-0.1.16.ebuild +++ b/sci-biology/samtools/samtools-0.1.16.ebuild @@ -1,10 +1,10 @@ # 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 $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.2 2011/07/18 01:50:51 jlec Exp $ -EAPI="2" +EAPI=2 -inherit toolchain-funcs +inherit multilib toolchain-funcs DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" HOMEPAGE="http://samtools.sourceforge.net/" @@ -12,11 +12,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" LICENSE="MIT" SLOT="0" -IUSE="" +IUSE="examples" KEYWORDS="~amd64 ~x86 ~x64-macos" src_prepare() { - sed -e '/^CFLAGS=/d' \ + sed \ + -e '/^CFLAGS=/d' \ -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \ -e "s/-shared/& \$(LDFLAGS)/" \ -i "${S}"/{Makefile,misc/Makefile} || die #358563 @@ -32,10 +33,15 @@ src_install() { dobin samtools || die dobin $(find misc -type f -executable) || die dolib.so libbam.so.1 || die + dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || 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 ${PN}.1 || die dodoc AUTHORS ChangeLog NEWS + + if use examples; then + insinto /usr/share/${PN} + doins -r examples || die + fi } diff --git a/sci-biology/samtools/samtools-0.1.17.ebuild b/sci-biology/samtools/samtools-0.1.17.ebuild new file mode 100644 index 000000000000..dbdcbb777a18 --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.17.ebuild @@ -0,0 +1,48 @@ +# 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-0.1.17.ebuild,v 1.1 2011/07/18 01:50:51 jlec Exp $ + +EAPI=4 + +inherit multilib 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="examples" +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 $(find misc -type f -executable) + + dolib.so libbam.so.1 + dosym libbam.so.1 /usr/$(get_libdir)/libbam.so + + insinto /usr/include/bam + doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h + + doman ${PN}.1 + dodoc AUTHORS ChangeLog NEWS + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} |