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

Package-Manager: portage-2.2.13/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

7 files changed, 104 insertions, 169 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/Manifest b/sci-biology/samtools/Manifest
index 2e4b88f0972b..f1ae3bfd3913 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,11 +1,31 @@
+-----BEGIN PGP SIGNED MESSAGE-----
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 DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac
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 EBUILD samtools-0.1.12.ebuild 827 SHA256 7f8dec32073313ec5a0a7801bcaf7675d74f4eefb2478b19615b22f1bd7e3708 SHA512 b67feeb1909327b6ab19fdb3167e602ab01bd075685bded200109b5def4ad80353f39c77dd8c8e1de1b6a43482acc0b85626951503f42f6dbf416bdbbf740851 WHIRLPOOL 58c4f8c129b41cf068fc08a225ebdd6fc6724efb0ba50eeb44ee0ec586d0634fd3a1fb24c89ee484bfc7cf5affad35c217192bf8eea4d548b220f8789329533d
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-EBUILD samtools-0.1.18-r3.ebuild 1416 SHA256 d6280443eabd20364429fee878ca3d12cd3e71043a8124fe15b53c0760ffeaaa SHA512 626318290d9630ae9610e12c91438b14bfd179ef34b0b5369f9fef50ea1f3b9b25b5312e3f355c2ed3f542a0395cc0661567d7f38f51534b9403478a48f0b69a WHIRLPOOL c88757966519ca99cd290395bb83b933192e3cf0d0591c7c0ef4c2fa8e619b49e4c083f30ef047d3d4de971ade42ddc8ec84a8e96618a796dc4c856f8b44efdc
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+EBUILD samtools-1.0.ebuild 1486 SHA256 6c53e74851376df0b0291ef08890a6a05254b1d8092daca2a3bcf5d548abf001 SHA512 bc44cb379fd8abef855f3da094a8923bf0cfee9e5c46ba8aa3d8ef1f8f16d3537bb83b4d40c31632c612ac66d6cc3d71693325497b95314c640dc4fdb1c2e46f WHIRLPOOL d5c12d50a5c6059770319ea8252b45acd3fbbae1a887cae5e46cea50970dfdf798da8620155dc5ef99b9ecbfda71b9f2761c55c29386f348849c22cdf8a6df38
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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
+}