sci-biology/velvet: Import Version BUmp from sci overlay, thanks mahn for the ebuild, #495094

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 98 insertions, 8 deletions

diff --git a/sci-biology/velvet/ChangeLog b/sci-biology/velvet/ChangeLog
index 802a15362468..c32155ab5bcb 100644
--- a/sci-biology/velvet/ChangeLog
+++ b/sci-biology/velvet/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/velvet
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.20 2013/03/12 12:13:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/ChangeLog,v 1.21 2013/12/28 23:19:35 jlec Exp $
+
+*velvet-1.2.10 (28 Dec 2013)
+
+  28 Dec 2013; Justin Lecher <jlec@gentoo.org> +velvet-1.2.10.ebuild:
+  Import Version BUmp from sci overlay, thanks mahn for the ebuild, #495094
 
   12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 70539d64e387..78fd89756ab6 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,16 +1,28 @@
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-Hash: SHA256
+Hash: SHA512
 
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 AUX velvet-1.0.18-gentoo-r1.diff 7879 SHA256 5a177e3d0b027069aa44ce97d964ab7f8ab97561f00aa9c4485f110dafb6fa89 SHA512 7aa112850c1d83220e1545ef29aa3e445ce55bc4334d062c353a5c5681723a3492c8dec52aeb58cfb5d464d1c748b721dc6400509fa872a48c428a2e0f9cdbf0 WHIRLPOOL 2d1017fc91e9e8d9753f8d1a39af54c1ce4712ffb9932527d48c32d08e8ab8a82eba7dd767b3866935bbb0e2d2bf2af84a0e4d1cf3c15ea5ad42e1097d107dbc
-DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e
+DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad WHIRLPOOL 69dcb5a6760b66eba65d054562e873d2c000dc57b487cdcf2c977bc1c0106bf027a79ff3b7e81da8a0f82b00635b755c26135b34de51cae34f4d276f15c2be74
+DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64
 EBUILD velvet-1.0.18-r1.ebuild 1617 SHA256 4c21b5d9e8b7b87b5e31fc6c794b9e4a5976bdc708597f8754a96cc63f79da16 SHA512 f92127496ccb3c5e0f676149307d0d06e35ce386908a60033a4ce3a1d3a819bf2def9ad5cf4fe8687fe22fc3c89a5896658c94b7b9d06072c4c5a1b48839d8e2 WHIRLPOOL 2cc7afd8a428c62c083fc0f9c4f35c85edd62c7ee150a3f8c82289a27a027be123e2131823c8f23f0af37b7a9fe7f3b05073f7589eff99d5f06c7dcd25829218
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+EBUILD velvet-1.2.10.ebuild 1891 SHA256 11823677176e0502b74e67707183d2d8db92ec96f6a6c8a20f9c93ed5f6558df SHA512 87acf4f35d9e17b2de59161b9988a724c69433d1d7f75018e4de45a21e7b926785c8de0fd278c3e04e609793ec37489255bcff18e535dd85382382c3c2f7e1d6 WHIRLPOOL b319edd78d3e29388a1dea2e637d0b53beebe40d7574501621588e7857ed7f57202ce026faeec867332dc9a324ac0da8b2512395e4f225a633abf8234fa679b8
+MISC ChangeLog 3173 SHA256 92a459663255453fb81a312b39afdb4bf14be7fce6865c24f74aaac03b3625d0 SHA512 fcacdb46103546ddca06d73704107828f7f18d2469abafc8c63e25c6c4ea466c45931cd4f2e11a4fc2ba9a18e8cd5c91f564b13bcf42597ed369b00c389adba1 WHIRLPOOL 82685cd51d29daf47230b7640407e7980bef9d7b0b9e2c61a32390cd708a134a9722f3b096cef029a23b27cf1afa9f3ec59892f9b951dce95fdfb059fbf8ea03
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diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
new file mode 100644
index 000000000000..47bbdb2d7b4d
--- /dev/null
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/velvet/velvet-1.2.10.ebuild,v 1.1 2013/12/28 23:19:35 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_P=${PN}_${PV}
+
+DESCRIPTION="A sequence assembler for very short reads"
+HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
+SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc openmp"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	doc? ( virtual/latex-base )"
+
+S="${WORKDIR}"/${MY_P}
+
+src_prepare() {
+	if ! use doc; then
+		sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
+	fi
+	elog "Upstream recommendes using -O3 in CFLAGS"
+	echo
+	elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
+	elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
+	elog "environment or /etc/make.conf, then re-emerge the package. For example:"
+	elog "  VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
+	MAKEOPTS+=" -j1"
+
+	if [[ $(tc-getCC) =~ gcc ]]; then
+		local eopenmp=-fopenmp
+	elif [[ $(tc-getCC) =~ icc ]]; then
+		local eopenmp=-openmp
+	else
+		elog "Cannot detect compiler type so not setting openmp support"
+	fi
+	append-flags -fPIC ${eopenmp}
+	append-ldflags ${eopenmp}
+
+	tc-export CC
+
+	MAKE_XOPTS=(
+		CC=$(tc-getCC)
+		CFLAGS="${CFLAGS}"
+		OPT="${CFLAGS}"
+	)
+	if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi
+	if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi
+}
+
+src_compile() {
+	emake "${MAKE_XOPTS[@]}"
+	emake "${MAKE_XOPTS[@]}" color
+}
+
+src_test() {
+	emake "${MAKE_XOPTS[@]}" test
+}
+
+src_install() {
+	dobin velvet{g,h,g_de,h_de}
+	insinto /usr/share/${PN}
+	doins -r contrib
+	dodoc Manual.pdf CREDITS.txt ChangeLog
+}