sci-biology/samtools: Install bcftools and vcfutils.pl pointed out by mahnmut

Package-Manager: portage-2.2.0_alpha169/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 68 insertions, 6 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 239b011da57c..444e7cb5b803 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/samtools
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.11 2013/03/11 16:56:12 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.12 2013/03/29 17:29:49 jlec Exp $
+
+*samtools-0.1.18-r3 (29 Mar 2013)
+
+  29 Mar 2013; Justin Lecher <jlec@gentoo.org> +samtools-0.1.18-r3.ebuild:
+  Install bcftools and vcfutils.pl pointed out by mahnmut
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 0b1ec94305f9..0d04a85e2ab0 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,17 +1,18 @@
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+Hash: SHA512
 
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 DIST samtools-0.1.18.tar.bz2 379306 SHA256 f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16 SHA512 fab570e0604f68046bb71a151b816315aeeeafbc970070f9b131975fe8fcf6ca0b5e02693bbde047bbe4d1500f6ff244d3d952219f69d5798af77ce9a3b643e3 WHIRLPOOL 6a430161ef382a501130436735495d3e97200b1018b3a77f5d367248d64179f2da7e84863a6699bdcff9d422d5c14a3f3f12d26a34a6a9e70d9ce4a358cb3f49
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+EBUILD samtools-0.1.18-r3.ebuild 1392 SHA256 4527a342df6e2dc51e3d00735aee7dd44d11fb8bc6a97963705edda54802328e SHA512 cb4f742b2e8405eeeb5eb2747279f84136f73b08a65903cbb2285bef965ca5eb0d3c505d3e15fae99db37f7b5784fe000f67d5284541494175eb9ad7da496971 WHIRLPOOL ff2b06e11fa8ca441979b1619f297405183d20e59bb234a08db836c28e8541dc341998bf72899863f17b7547d6c2052b4f1d24c04548a81f19064b8fad1eeea3
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diff --git a/sci-biology/samtools/samtools-0.1.18-r3.ebuild b/sci-biology/samtools/samtools-0.1.18-r3.ebuild
new file mode 100644
index 000000000000..3c4c954309dc
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.18-r3.ebuild
@@ -0,0 +1,56 @@
+# 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 1.1 2013/03/29 17:29:49 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 ~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
+}