sci-biology/samtools: Version Bump, #523224; drop old

(Portage version: 2.2.13/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

6 files changed, 78 insertions, 163 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 4b723ff0aaa6..ddb2c5c7e66e 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -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 <jlec@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)
 
diff --git a/sci-biology/samtools/samtools-0.1.18-r2.ebuild b/sci-biology/samtools/samtools-0.1.18-r2.ebuild
deleted file mode 100644
index 8255f98c5582..000000000000
--- a/sci-biology/samtools/samtools-0.1.18-r2.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r2.ebuild,v 1.2 2013/12/06 12:44:16 jlec Exp $
-
-EAPI=5
-
-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 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="sys-libs/ncurses"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	sed \
-		-e '/^CC/s:=:?=:g' \
-		-e "/^LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \
-		-e '/^CFLAGS=/s:=:?=:' \
-		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
-		-e "s/-shared/& \$(LDFLAGS)/" \
-		-i "${S}"/{Makefile,misc/Makefile} || die #358563
-	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
-	tc-export CC
-}
-
-src_compile() {
-	emake dylib
-	emake
-}
-
-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
-}
diff --git a/sci-biology/samtools/samtools-0.1.18-r3.ebuild b/sci-biology/samtools/samtools-0.1.18-r3.ebuild
deleted file mode 100644
index a4c7a3bbab60..000000000000
--- a/sci-biology/samtools/samtools-0.1.18-r3.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18-r3.ebuild,v 1.2 2013/12/06 12:44:16 jlec Exp $
-
-EAPI=5
-
-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 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="sys-libs/ncurses"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	sed \
-		-e '/^CC/s:=:?=:g' \
-		-e "/^LIBCURSES/s:=.*$:= $(pkg-config --libs ncurses):g" \
-		-e '/^CFLAGS=/s:=:?=:' \
-		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
-		-e "s/-shared/& \$(LDFLAGS)/" \
-		-i "${S}"/{bcftools,misc,}/Makefile || die #358563
-	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
-
-	tc-export CC
-}
-
-src_compile() {
-	emake dylib
-	emake
-}
-
-src_install() {
-	dobin samtools $(find bcftools misc -type f -executable)
-
-	dolib.so libbam.so.1
-	dosym libbam.so.1 /usr/$(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
-}
diff --git a/sci-biology/samtools/samtools-0.1.18.ebuild b/sci-biology/samtools/samtools-0.1.18.ebuild
deleted file mode 100644
index 37c80eecebf5..000000000000
--- a/sci-biology/samtools/samtools-0.1.18.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.18.ebuild,v 1.2 2013/12/06 12:44:16 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 ~amd64-linux ~x86-linux ~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
-}
diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
index a105de74248f..acda6ff8ddf9 100644
--- a/sci-biology/samtools/samtools-0.1.19-r2.ebuild
+++ b/sci-biology/samtools/samtools-0.1.19-r2.ebuild
@@ -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_prepare() {
 }
 
 src_compile() {
-	local _ncurses="$(pkg-config --libs ncurses)"
+	local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
 	emake dylib LIBCURSES="${_ncurses}"
 	emake LIBCURSES="${_ncurses}"
 }
diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild
new file mode 100644
index 000000000000..ed94621021cf
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.0.ebuild
@@ -0,0 +1,68 @@
+# 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
+}