Version bump, drop old

Package-Manager: portage-2.2_rc86/cvs/Linux x86_64

4 files changed, 58 insertions, 52 deletions

diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog
index 111c6530f1ef..7b1e8a197e32 100644
--- a/sci-biology/shrimp/ChangeLog
+++ b/sci-biology/shrimp/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/shrimp
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.11 2010/08/09 18:19:28 xarthisius Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.12 2011/02/03 00:13:49 weaver Exp $
+
+*shrimp-2.1.0 (03 Feb 2011)
+
+  03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> -shrimp-1.2.1.ebuild,
+  +shrimp-2.1.0.ebuild:
+  Version bump, drop old
 
   09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> shrimp-2.0.1.ebuild:
   Fix dependency on openmp.
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index 828d8c04eafc..96122f1c5d6b 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -1,20 +1,8 @@
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-Hash: SHA1
-
-DIST SHRiMP_1_2_1.src.tar.gz 102426 RMD160 59c241bfa0570b9dcf9222f6b8991ba1f88ac28a SHA1 6b54b5aa38f4d79cc3fd1fc97cd327f650f0d9ee SHA256 8fe55ca7cda3b90e8daa094fa3b4ee902271779fb5eb6a6d6f31bb4ad9a4db0a
 DIST SHRiMP_1_3_1.src.tar.gz 120929 RMD160 399455b93be51047958945c767a3bdd31dada88e SHA1 ce571eb23ce3172fd1303ffd71deee652e9d395e SHA256 a0847d1e05ca4c277d7be95f315b5f7d12fad0852324985660fe9ea1820487b9
 DIST SHRiMP_2_0_1.src.tar.gz 158535 RMD160 9153bb3b1cb8648a74df431537b38efa4267929a SHA1 b6b54a2990fc5193b72f2a08f47f95b527fabde3 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
-EBUILD shrimp-1.2.1.ebuild 839 RMD160 88ecf132a12ca3369417db49aebe3dab18b123f9 SHA1 c469ada9ad92df5fc7a8cb8c05c981bbb7e01f98 SHA256 4d6aabd86b1b726fcc0d1491fdc808fd6952656f7a6f770f9e2a059cdcc5809f
+DIST SHRiMP_2_1_0.src.tar.gz 189121 RMD160 846b9c014c5d961f1c86e7c169a14e9be01c25e7 SHA1 52afe3673f2205cb79000999daf247cef808e003 SHA256 72a414fcbc528e98af70967942ecf32b377df0582c8076a0bf32c95fa8a8c39e
 EBUILD shrimp-1.3.1.ebuild 845 RMD160 dbabe4f8787f2be0d9afeb5704d34815e2cb32a6 SHA1 cc36b8fbf230f6d460a162785c05beccf7a534b8 SHA256 148eee6a913bb3806918369c26c876b6d4bcd81b65de4ad65d49c95d738c305e
 EBUILD shrimp-2.0.1.ebuild 1206 RMD160 8bf9c620192fcb7207b4d4fdabd1ccf455daf451 SHA1 891abaaac2fc483edc1b4895cc1cbc1732e8d5e4 SHA256 29aba3f289269f75699344ede422ab4e0598634d9f1bd6ca54b40cf9d01a3895
-MISC ChangeLog 1698 RMD160 62c865bb9dee3c59e7c4badad0662af50ba9455a SHA1 2acc0bd7b2f8876d0758ca5ebabe7100a56acdba SHA256 3c3911625eb6f8b6be1cd72351cd5315896ec8dc3d053d46d0d321e8433b3cd0
+EBUILD shrimp-2.1.0.ebuild 1215 RMD160 2fc65900b3b0357932d9a5056b0cc20b510b9d7c SHA1 2f9e83cc7e26db66d0853c7f587a14bb0f354d0e SHA256 35b4799dd3431956998974831d27703081c0019f94343770885d29db1c9ef81e
+MISC ChangeLog 1845 RMD160 a84707ca5c9117774fcf64aac8cbc196ee334c18 SHA1 6f6750ddc1e85c1affc379a072f0a8bb56be82f9 SHA256 eb4b4ea1385c09ccd2dd737b68a70ecc21ba296bd40f240cf4bff2ca4eb85ffa
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/shrimp/shrimp-1.2.1.ebuild b/sci-biology/shrimp/shrimp-1.2.1.ebuild
deleted file mode 100644
index 12291b1270e1..000000000000
--- a/sci-biology/shrimp/shrimp-1.2.1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-1.2.1.ebuild,v 1.5 2009/12/09 18:52:14 weaver Exp $
-
-EAPI="2"
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="as-is"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}/SHRiMP_${MY_PV}"
-
-src_prepare() {
-	sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die
-	sed -i -e '1 a CXXFLAGS+= -O3 -mmmx -msse -msse2' \
-		-e 's/-static//' "${S}/Makefile" || die
-}
-
-src_install() {
-	rm bin/README
-	dobin bin/* || die
-	insinto /usr/share/${PN}
-	doins -r utils || die
-	dodoc HISTORY README TODO
-}
diff --git a/sci-biology/shrimp/shrimp-2.1.0.ebuild b/sci-biology/shrimp/shrimp-2.1.0.ebuild
new file mode 100644
index 000000000000..b6e235263f49
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.1.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.1.0.ebuild,v 1.1 2011/02/03 00:13:49 weaver Exp $
+
+EAPI="2"
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=sys-devel/gcc-4.3[openmp]"
+RDEPEND="${DEPEND}"  # -lgomp
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	tc-has-openmp || die "At least gcc-4.3 is required for openmp support."
+}
+
+src_prepare() {
+	sed -i -e '1 a #include <stdint.h>' common/dag_glue.cpp || die #294811
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+}
+
+src_compile() {
+	append-flags -fopenmp -O3 # per instructions in BUILDING
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die
+}
+
+src_install() {
+	dobin bin/* || die
+	insinto /usr/share/${PN}
+	doins -r utils || die
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING || die
+}