sci-biology/shrimp: Vesion Bump

Package-Manager: portage-2.2.0_alpha141/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

3 files changed, 76 insertions, 5 deletions

diff --git a/sci-biology/shrimp/ChangeLog b/sci-biology/shrimp/ChangeLog
index 4f57d4aba634..a3af6b4ff9ef 100644
--- a/sci-biology/shrimp/ChangeLog
+++ b/sci-biology/shrimp/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/shrimp
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.15 2012/10/18 18:00:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/ChangeLog,v 1.16 2012/10/18 18:17:38 jlec Exp $
+
+*shrimp-2.2.3 (18 Oct 2012)
+
+  18 Oct 2012; Justin Lecher <jlec@gentoo.org> +shrimp-2.2.3.ebuild:
+  Vesion Bump
 
   18 Oct 2012; Justin Lecher <jlec@gentoo.org> -shrimp-1.3.1.ebuild,
   shrimp-2.0.1.ebuild, shrimp-2.1.0.ebuild:
diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
index 687e7e972b6d..a5c14b0fbd05 100644
--- a/sci-biology/shrimp/Manifest
+++ b/sci-biology/shrimp/Manifest
@@ -3,15 +3,17 @@ Hash: SHA256
 
 DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63
 DIST SHRiMP_2_1_0.src.tar.gz 189121 SHA256 72a414fcbc528e98af70967942ecf32b377df0582c8076a0bf32c95fa8a8c39e SHA512 01a54dbcb645bfa55ec280d932cc947cab9b6f5266d273d8ea4103cb298e747da00aa04b56753f880d6de11663d9c4219b2402f84d5c15ebe4f1c5bb94e80a8a WHIRLPOOL d0f87dbad1a61c83527be166181eabd491fc3e5a2bd6e22aacd4b369146940e2d843b44ab6e6e9b7c092afe6c08b1cb7b060e3944e47f3d3c87acc634a2c7f36
+DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
 EBUILD shrimp-2.0.1.ebuild 1267 SHA256 4685094dae4cd65bffa0da56634350599c5ec4748111e3ce81942b1eea2b63d0 SHA512 96698ffcabc0f57c763e080e935ebb89b19499786c9dc6cdda1cc04f71224cfd9745965ca48f396da501b099781c1fa66405332fac0c534eb969d2dcd7462ed4 WHIRLPOOL 042167c616f661495139539dc2936c3e75389da400f02400d85771375014c510b25f7d4645db667c78790d1ffd7df723ce1dd58532e3fcd42f68a4076b8fd3d0
 EBUILD shrimp-2.1.0.ebuild 1258 SHA256 fd9cb865e3fc3afec5ffd40134f94be6fe72d8c9be7ea211eff27a1298770b31 SHA512 6a7a4e416b9b00d1973e810a4026aa926516a7ba5046959bb90dbbc574ceb8fd34293f9995bd6cc55322612b10d4f2cca681ee0cde9541e2b903d3f685a56bad WHIRLPOOL 05205feb28fab7159797d51e539e67f55c3676836890fda8e984740828867b2c5a4d26468a22552350c968e4948ac05e4d633e31d42c1b95a9f33bf26d2ed920
-MISC ChangeLog 2206 SHA256 43d33b3de640d125afc013ae32e2ea29d46012de485d4fa4a85d14b34f0e0fc3 SHA512 dbb02d052f48e1f7b12ca04941a34fd36238cc8fb0c2c868fb16da523c16ca62974d02eb85701db4aa92479df6857bb053c865ecc4574b5aa01b56522f13b46a WHIRLPOOL ffc4aea77a8886891e57a1f3b0d217ca2ec3cba106cf7fab66aaff80e710e6d652cd2e6e419c997183942d54df779f01114ef2a3387b752155b48b9fa39e766d
+EBUILD shrimp-2.2.3.ebuild 1558 SHA256 be720864d3e4da68976225a6f2cf72683a67ec2a0e46414ca161d838940f1eb2 SHA512 a98fe2daf136656378baa5caea0241ae66896ac85ca502af10f0f7f1becb838cfb9c067e0341fa0f6bbd2169711f03e3a1ad69eabf9f8188ef52960b7025b83c WHIRLPOOL 81b9b701bda5a2283aac36a22b076754af60f3b3c88df292a317366fea53b8e5815e87a109668cd63937526b8838cd9b9998c53e98a1d4762796665b9fc32c79
+MISC ChangeLog 2319 SHA256 345021fa88912b6a06b167cdcdd1ae80e8e7b18648a5046f8141f7d7cbda3f80 SHA512 72bd6e0d6e089a764ce14dbec54c3406df49ba60d9afc5c7eb9369db9eb3fd56aa2ca06f8c8d8e85a86efb95b0f501404d93eee2a113e5a1a50fc6b0e0afc28e WHIRLPOOL 766adba4ce831c21279e022bda4b9c3ece20cc8b29434984046eb864ac5dffdbf69aa31c605abb792a0e96b5ead51bc854d4c757e8ced545df5e26fb847051fe
 MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
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diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
new file mode 100644
index 000000000000..ce8cbe51b610
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.1 2012/10/18 18:17:38 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit flag-o-matic python 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"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+	python_convert_shebangs -r -- 2 utils
+}
+
+src_compile() {
+	append-flags -fopenmp
+	if ! use custom-cflags; then
+		append-flags -O3
+		replace-flags -O2 -O3
+	fi
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	local i
+	dobin bin/* utils/split-contigs utils/temp-sink
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
+
+	pushd utils > /dev/null
+	for i in *py; do
+		newbin ${i} ${i%.py}
+	done
+
+	rm *.py *.o *.c split-contigs temp-sink || die
+	insinto /usr/share/${PN}
+	doins -r *
+}