Version bump

Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64

3 files changed, 62 insertions, 7 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 99890c78a18f..bafb11674633 100644
--- a/sci-biology/samtools/ChangeLog
+++ b/sci-biology/samtools/ChangeLog
@@ -1,6 +1,11 @@
 # 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 1.7 2011/07/18 01:50:51 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.8 2011/09/26 15:18:39 weaver Exp $
+
+*samtools-0.1.18 (26 Sep 2011)
+
+  26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +samtools-0.1.18.ebuild:
+  Version bump
 
 *samtools-0.1.17 (18 Jul 2011)
 
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index fad81b32b286..c8477b96051a 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,19 +1,21 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA1
 
 DIST samtools-0.1.12a.tar.bz2 355633 RMD160 e2732e61b216bc2d8e6a1c81aa91c34f296cef29 SHA1 d517cd189aa714251a0e43cb83dea3ae0f29bffa SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac
 DIST samtools-0.1.16.tar.bz2 379809 RMD160 2cbc5c4f765a870b44a949d28ec8f23ceb96f954 SHA1 4f00dad58f707efb84a4d0144b6245e4da4077e5 SHA256 ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726
 DIST samtools-0.1.17.tar.bz2 373930 RMD160 0921e733358ccf01d316dff2b797957f4f2cfb7b SHA1 4d2ef4273d9f71cd1f504f43c596970845d78718 SHA256 aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e
+DIST samtools-0.1.18.tar.bz2 379306 RMD160 0301de58e31c7529a2535086be0cc7d93778ede8 SHA1 77be35df7a90c288a003ff826ba99aef53b2fbe6 SHA256 f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16
 EBUILD samtools-0.1.12.ebuild 803 RMD160 cb341ebd2cfe8b713ded11d75c5a32501f9b8480 SHA1 35c415aece9b650d80947ebc4c2aea32aed996c1 SHA256 352173d51993cbe61f3058330ed3accf0c2b9e79f0bc70e87f95c3824efca84c
 EBUILD samtools-0.1.12a-r1.ebuild 1313 RMD160 80de893c09041811b69535780ca3ed962edea40a SHA1 aa26ea497f4b3ccce38bbc370d9b97972bf67e74 SHA256 bf7cd173267b4aeaa34d64b1fab9e67760e2efbeda17d93e9aeb02cf001b6a1b
 EBUILD samtools-0.1.16.ebuild 1309 RMD160 dde64f340a4424d84847583efdc3e3b5fa3361e8 SHA1 9db17da03cea41eba79293399bf53f46bbff37ea SHA256 52786cd40976d1c44bd0443309bd1bd95eab44c52f2f084be3599a21cbe8a779
 EBUILD samtools-0.1.17.ebuild 1255 RMD160 b2e75245ae7dd346f8f254725d94b3e02a8d5ea7 SHA1 abead18f1e64960076a567a83d0cd8ab842dde75 SHA256 f000247b1df2a3d78d0bb1e56e5357e8ecd0ea138da40b8432dd1b1b57e827a1
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+EBUILD samtools-0.1.18.ebuild 1257 RMD160 58f623d7616246f2c45b69be5436dd5da571ca26 SHA1 963893ba092082261ea21f2fbdf46ecb5b46be65 SHA256 6d5f5ccb99180e5b9291d10f135be7b56a5361742e96af572f9cee9fe6ce2256
+MISC ChangeLog 1662 RMD160 b002995d899a8c3bdf1f6fe554a96ab50008b3ed SHA1 125fa5fcb0b0bdb265eb35d841b852f141b599e7 SHA256 3ff026e760302aae225fbd987dc03804edefb37273f150090bdc0d07c08658f7
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
+Version: GnuPG v1.4.11 (GNU/Linux)
 
-iEYEAREKAAYFAk4jkYEACgkQgAnW8HDreRbM5ACgy7dZVGVTLotpfT7JwYu+seGL
-0B4AoJReB1RRP1X7klSuQH7ItzLRpxBi
-=+y2t
+iEYEARECAAYFAk6Al9QACgkQ8xSwyhbn2Ob5cACbBQM0x7X+rdhwWgGZ9yVJQV6a
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diff --git a/sci-biology/samtools/samtools-0.1.18.ebuild b/sci-biology/samtools/samtools-0.1.18.ebuild
new file mode 100644
index 000000000000..40147cfdd0ef
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.18.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-0.1.18.ebuild,v 1.1 2011/09/26 15:18:39 weaver 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
+}