reinit the tree, so we can have metadata

4 files changed, 151 insertions, 0 deletions

diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
new file mode 100644
index 000000000000..f23b17a02902
--- /dev/null
+++ b/sci-biology/shrimp/Manifest
@@ -0,0 +1,7 @@
+DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63 SHA512 1cb5d46d59102502acb26c33f1d5537644268704145f6e2ae7428aeaba6681cf1e63f7924d8ee696431675f2c4627da46fd0171f25bbb3296d247339c2d709eb WHIRLPOOL 0091c399830413a97b634d012b68015443ae04e4b3d6ffeb1665e3610226accfba9e21a2ed84935bb0bc4bca9dd92e122e96b905c96274255ad9b9527c1491fc
+DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a
+EBUILD shrimp-2.0.1.ebuild 1279 SHA256 20b62cd9cad1523affab305c820b5618c4cfa4e27fc1407abbc3131dca94e25e SHA512 d16226d78b627809be5dc8b5fb39e552a71ceb6a8834ad68650fd9d3c69b425ee2e29a56f1e9b1b59e56f43a149169cc75c6694fe35c18ebc052fa7d30b6902d WHIRLPOOL f08c43d86f1ea15edd0efb51fae94fd53d94931354d11abcb1a4086bdde4f10a98b4d262434a3849e777f25a0bb51ab994ae316b3d647bc6d3ecfdc9025b4129
+EBUILD shrimp-2.2.3.ebuild 1818 SHA256 04abbc318833647f7876780629cae1a29c418cb632bf1a822b6fd1c3d9000130 SHA512 2bfdb6f1cf7678dc9fafd66c25c07f55671f39600a44c606bac33652806105ff448d231202fb405307a0a49716557aa7cc63d371163821af2d919422ff9e2e6f WHIRLPOOL 391323a0d760243efcf66df9326b84f150f7d647228fd85ddfa372aeaa5c35e1e2bcfcbdc6970a6ca8e451cde3fbcc57dfb520348089fb2ae84deedfba17289b
+MISC ChangeLog 2477 SHA256 b9e8966a55fe6448d690657ea9d6d08953ac2344f4d05312427e943d0f3d5170 SHA512 b1a90ff02a903e7af3749c812be39683e059682995daed5ac7186cf53cf70f5dead1fe2ce6c9021fa9840b774b2826c01ab06407561514e8bc41bfc13da37998 WHIRLPOOL 1bb7d76b98f12a65bbe1ff961bcbfc2d3427ea6254d0b9219bb1f565062ef12642d8206d9aa2cbc02a120c24c1c468d781792a403c7ec25f64bf67e43b7e0f3f
+MISC ChangeLog-2015 3578 SHA256 4383747a10a276d21052452177296d6b06e005288e4925766fbd935c757be911 SHA512 1540a70ac90b11edd4d1eb916ea10e0fecf63eb5f72e0d16dda9226541d0d7338288f41ff6202d946d561c5492b59fa84608ae50a0e7a7c41d6283e5f57d0489 WHIRLPOOL a8ab0ed4c66cc9c6b6a1536401709ece68dbf59192ecf955ee131bfd08beca0ea2aa567cf5fb89de1be8d8c1ccea4456702dc6b4e6e402de848885ce2514cf5c
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/shrimp/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
new file mode 100644
index 000000000000..c71aa047c1a7
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+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="shrimp"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="custom-cflags"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="
+	!sci-biology/emboss
+	!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+}
+
+src_prepare() {
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+}
+
+src_compile() {
+	append-flags -fopenmp
+	use custom-cflags || append-flags -O3 # per instructions in BUILDING
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	rm bin/README
+	dobin bin/*
+	insinto /usr/share/${PN}
+	doins -r utils
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING
+}
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..2b57b032a1b2
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit flag-o-matic python-single-r1 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="shrimp"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags +cpu_flags_x86_sse2"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}
+	${PYTHON_DEPS}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_pretend() {
+	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
+}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e '1 a #include <stdint.h>' \
+		-i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed \
+		-e "s/LDFLAGS/LIBS/" \
+		-e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' \
+		-i Makefile || die
+
+	append-flags -fopenmp
+	if ! use custom-cflags; then
+		append-flags -O3
+		replace-flags -O* -O3
+	fi
+	tc-export CXX
+
+	cd utils || die
+	sed -e '/^#!/d' -i *py || die
+	sed -e '1i#!/usr/bin/python' -i *py || die
+}
+
+src_compile() {
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	local i
+	newdoc bin/README README.bin && rm bin/README
+	dobin bin/* utils/split-contigs utils/temp-sink
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
+
+	pushd utils > /dev/null
+
+	python_doscript *py
+
+	rm *.py *.o *.c split-contigs temp-sink || die
+	insinto /usr/share/${PN}
+	doins -r *
+}