Version BUmp, #365265

(Portage version: 2.2.0_alpha30/cvs/Linux x86_64)

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
+}