Version Bump, #375519

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

6 files changed, 93 insertions, 25 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 99a1483e3bfc..99890c78a18f 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 1.6 2011/04/30 11:12:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.7 2011/07/18 01:50:51 jlec Exp $
+
+*samtools-0.1.17 (18 Jul 2011)
+
+  18 Jul 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild,
+  samtools-0.1.12a-r1.ebuild, samtools-0.1.16.ebuild, +samtools-0.1.17.ebuild:
+  Version Bump, #375519
 
 *samtools-0.1.16 (30 Apr 2011)
 
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index 14ae3e7b2f5c..fad81b32b286 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,17 +1,19 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 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
-EBUILD samtools-0.1.12.ebuild 805 RMD160 74c865b783d013ade440d977256b6a5b38eb1494 SHA1 6dd046b03fc30de19ff7b066395b0e200477d8aa SHA256 6bfe99c01a90b38a78382ebe11d140f0fa056f62bcdca9b90eddd22c0b86059c
-EBUILD samtools-0.1.12a-r1.ebuild 1208 RMD160 c4823b02daa32f5a45300254e2a5a4a1ab48ab6d SHA1 80d8feb4c7e8c6c691fb6ffb1de0d45ea34f3b98 SHA256 6d467bcf0ff455e078f0a39bdfde7ae5e43fa7b6caf2f9af501c894584639270
-EBUILD samtools-0.1.16.ebuild 1204 RMD160 d1c1679f1508e50bbd26da2789a6a3cc1da02d10 SHA1 71e15a36116ec7957d97cbd12986dba4a2e4803c SHA256 26f11d3b82fb6ece5a120d014dbf6f38e7fd83e8072ed74589a45af7587caa34
-MISC ChangeLog 1330 RMD160 2e09aa3a042277210c86db59ca75af88dad647a1 SHA1 8d27189209ad0ce47144c7262c9682613c0a9f43 SHA256 934af846108343e423dfdae491bd9e9f3fa2614c847e02d8c2fc2a9c498d71c0
+DIST samtools-0.1.17.tar.bz2 373930 RMD160 0921e733358ccf01d316dff2b797957f4f2cfb7b SHA1 4d2ef4273d9f71cd1f504f43c596970845d78718 SHA256 aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e
+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
+MISC ChangeLog 1537 RMD160 a86fc16522aac9e8c96a0f28c914829c6f379224 SHA1 20f842e92727faec4df400dc28301dcd27379f8d SHA256 e39f26524accbf7df4e2766814fc92daec1e7454f814d26786ed724371763a67
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk277rcACgkQgAnW8HDreRZYlwCeIJsd5scegjjDAFGLmTrvAMhR
-KbgAoKpvzUCp/o4dRhtWxH8e/26JEy7o
-=ommx
+iEYEAREKAAYFAk4jkYEACgkQgAnW8HDreRbM5ACgy7dZVGVTLotpfT7JwYu+seGL
+0B4AoJReB1RRP1X7klSuQH7ItzLRpxBi
+=+y2t
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild
index bd221c67fb5f..9cdeed8532b5 100644
--- a/sci-biology/samtools/samtools-0.1.12.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12.ebuild
@@ -1,8 +1,8 @@
 # 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 1.4 2011/04/30 11:12:50 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.5 2011/07/18 01:50:51 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
 MY_P="${P}a"
 
diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
index 8f9f30d2e6df..5c689a266cee 100644
--- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
@@ -1,10 +1,10 @@
 # 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 1.2 2011/04/30 11:12:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.3 2011/07/18 01:50:51 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
-inherit toolchain-funcs
+inherit toolchain-funcs multilib
 
 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
 HOMEPAGE="http://samtools.sourceforge.net/"
@@ -12,11 +12,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"
-IUSE=""
+IUSE="examples"
 KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 src_prepare() {
-	sed -e '/^CFLAGS=/d' \
+	sed \
+		-e '/^CFLAGS=/d' \
 		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
 		-e "s/-shared/& \$(LDFLAGS)/" \
 		-i "${S}"/{Makefile,misc/Makefile} || die #358563
@@ -32,10 +33,15 @@ src_install() {
 	dobin samtools || die
 	dobin $(find misc -type f -executable) || die
 	dolib.so libbam.so.1 || die
+	dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || 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 ${PN}.1 || die
 	dodoc AUTHORS ChangeLog NEWS
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples || die
+	fi
 }
diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild
index 949d0f92aa9d..a2181d1f6cfc 100644
--- a/sci-biology/samtools/samtools-0.1.16.ebuild
+++ b/sci-biology/samtools/samtools-0.1.16.ebuild
@@ -1,10 +1,10 @@
 # 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.2 2011/07/18 01:50:51 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
-inherit toolchain-funcs
+inherit multilib toolchain-funcs
 
 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
 HOMEPAGE="http://samtools.sourceforge.net/"
@@ -12,11 +12,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
 
 LICENSE="MIT"
 SLOT="0"
-IUSE=""
+IUSE="examples"
 KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 src_prepare() {
-	sed -e '/^CFLAGS=/d' \
+	sed \
+		-e '/^CFLAGS=/d' \
 		-e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
 		-e "s/-shared/& \$(LDFLAGS)/" \
 		-i "${S}"/{Makefile,misc/Makefile} || die #358563
@@ -32,10 +33,15 @@ src_install() {
 	dobin samtools || die
 	dobin $(find misc -type f -executable) || die
 	dolib.so libbam.so.1 || die
+	dosym libbam.so.1 /usr/$(get_libdir)/libbam.so || 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 ${PN}.1 || die
 	dodoc AUTHORS ChangeLog NEWS
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples || die
+	fi
 }
diff --git a/sci-biology/samtools/samtools-0.1.17.ebuild b/sci-biology/samtools/samtools-0.1.17.ebuild
new file mode 100644
index 000000000000..dbdcbb777a18
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.17.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-0.1.17.ebuild,v 1.1 2011/07/18 01:50:51 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 ~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
+}