Version BUmp, #365265

Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64

5 files changed, 67 insertions, 11 deletions

diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog
index 8ac0f6446300..99a1483e3bfc 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 1.5 2011/03/14 09:37:27 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.6 2011/04/30 11:12:49 jlec Exp $
+
+*samtools-0.1.16 (30 Apr 2011)
+
+  30 Apr 2011; Justin Lecher <jlec@gentoo.org> samtools-0.1.12.ebuild,
+  samtools-0.1.12a-r1.ebuild, +samtools-0.1.16.ebuild:
+  Version BUmp, #365265
 
 *samtools-0.1.12a-r1 (14 Mar 2011)
 
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index c92f6c8c9e3d..14ae3e7b2f5c 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,5 +1,17 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST samtools-0.1.12a.tar.bz2 355633 RMD160 e2732e61b216bc2d8e6a1c81aa91c34f296cef29 SHA1 d517cd189aa714251a0e43cb83dea3ae0f29bffa SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac
-EBUILD samtools-0.1.12.ebuild 825 RMD160 945e352ee7f8a2c0726056fa12df4b0d1d0606c8 SHA1 b7d91116e37c1c990e3bbb816b0aad4239f02dff SHA256 b99a0a6d5b03c44f70324eaf5fa7dabad68ddef8707d6e384585d2cc9bab5a45
-EBUILD samtools-0.1.12a-r1.ebuild 1213 RMD160 2f5f8c2d4f86aaacdd40fbf1eb6acbfb89a84687 SHA1 e25dce211a2af68a5eb35278dcbc6b68e600d90b SHA256 93d470593346d56c81914e25dc31b67f8a5646b76bb1237238897f4225abf751
-MISC ChangeLog 1153 RMD160 b6584e284a2bba7ccb782a3193f3959d021d8f4b SHA1 369cb4024d7318ca7e52251d1c13bb7851c8d571 SHA256 0ee56ddba88d63c598bda3fe5e15696bff6e384471821bb9985ea41b38609485
+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
 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
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild
index a2953ebbd51c..bd221c67fb5f 100644
--- a/sci-biology/samtools/samtools-0.1.12.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12.ebuild
@@ -1,13 +1,13 @@
 # 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 1.3 2011/02/17 09:05:13 tomka Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.4 2011/04/30 11:12:50 jlec Exp $
 
 EAPI="2"
 
 MY_P="${P}a"
 
 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
-HOMEPAGE="http://${PN}.sourceforge.net/"
+HOMEPAGE="http://samtools.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
 
 LICENSE="MIT"
@@ -15,9 +15,6 @@ SLOT="0"
 IUSE=""
 KEYWORDS="amd64 x86"
 
-DEPEND=""
-RDEPEND=""
-
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
diff --git a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
index 963f27c77d57..8f9f30d2e6df 100644
--- a/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
+++ b/sci-biology/samtools/samtools-0.1.12a-r1.ebuild
@@ -1,6 +1,6 @@
 # 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 1.1 2011/03/14 09:37:27 xarthisius Exp $
+# $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 $
 
 EAPI="2"
 
@@ -33,7 +33,7 @@ src_install() {
 	dobin $(find misc -type f -executable) || die
 	dolib.so libbam.so.1 || die
 	insinto /usr/include/bam
-	doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h|| die
+	doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
 	insinto /usr/share/${PN}
 	doins -r examples || die
 	doman ${PN}.1 || die
diff --git a/sci-biology/samtools/samtools-0.1.16.ebuild b/sci-biology/samtools/samtools-0.1.16.ebuild
new file mode 100644
index 000000000000..949d0f92aa9d
--- /dev/null
+++ b/sci-biology/samtools/samtools-0.1.16.ebuild
@@ -0,0 +1,41 @@
+# 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 $
+
+EAPI="2"
+
+inherit 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=""
+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 || die
+	dobin $(find misc -type f -executable) || die
+	dolib.so libbam.so.1 || die
+	insinto /usr/include/bam
+	doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
+	insinto /usr/share/${PN}
+	doins -r examples || die
+	doman ${PN}.1 || die
+	dodoc AUTHORS ChangeLog NEWS
+}