A bioinformatics library for haskell (requested by Martin MOKREJŠ).

(Portage version: 2.2.1_p20/cvs/Linux x86_64, signed Manifest commit with key 611FF3AA)

4 files changed, 98 insertions, 0 deletions

diff --git a/dev-haskell/bio/ChangeLog b/dev-haskell/bio/ChangeLog
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+# ChangeLog for dev-haskell/bio
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-haskell/bio/ChangeLog,v 1.1 2013/09/12 20:19:20 slyfox Exp $
+
+*bio-0.5.3 (12 Sep 2013)
+
+  12 Sep 2013; Sergei Trofimovich <slyfox@gentoo.org> +bio-0.5.3.ebuild,
+  +metadata.xml:
+  A bioinformatics library for haskell (requested by Martin MOKREJŠ).
diff --git a/dev-haskell/bio/Manifest b/dev-haskell/bio/Manifest
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+DIST bio-0.5.3.tar.gz 103707 SHA256 42c8f9b83fea6bf51356afe1251910ba4421e0af0bb4f26431eaf385971d7eed SHA512 fbe09240a600abbcac952f52f05f28f9b305a1ae3def8b4144bd73bdb160acfbe5457086ef829057d5a73df1df5061668487b2ca5621df73628c8c4990b6b544 WHIRLPOOL 84d057c68b0fbf899594470e171f883b92def29f0f7f607b08d0d419dd01c5f2e0f6054f93387c32b6b7ffdd1ceb6e84ef6b8cfe5faaee1f89c2e8b10837dcb8
+EBUILD bio-0.5.3.ebuild 1375 SHA256 ecf9ceec6bda42efbdc69ff61de7537e9410c04162d553efa769c495cf4e8b98 SHA512 82fee07894b9e332aac30e82bd367c0f0c3e02f61d5ad5f5b70542244b522eba96bb83435bffb4bdff6cdffe1c8823181277be00a83fab7892a5d6e65e6534e2 WHIRLPOOL 9f3176b3586f79dc6342090b8faadabc9c1a0f34753bcf11b9080798033325bb253cd8a6a75ad7a8e8e2d3160a8297ae883b93d1b2509dc12d1df452343decd1
+MISC metadata.xml 1122 SHA256 aaafdc9895fe7b024ed53b6c43689db3d3b4521a3d1f95cfa9a4efa79a9039c6 SHA512 3ea3be892112d9141e04990e90d59a6a4605a4b884a7395ba179fe43068fb2a9c9c70cd3338ceecd615831f5474620768d529e355f72c1fedc652c82f2530841 WHIRLPOOL db24da3d68a86d0a77a825d27f8fba03aeab0235723d485b878fa7cb5473b60ea291d1541a7acd95c205cfc5b570caaa852c23a41b2a1076eecd79c16bb36c14
diff --git a/dev-haskell/bio/bio-0.5.3.ebuild b/dev-haskell/bio/bio-0.5.3.ebuild
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+++ b/dev-haskell/bio/bio-0.5.3.ebuild
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+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-haskell/bio/bio-0.5.3.ebuild,v 1.1 2013/09/12 20:19:20 slyfox Exp $
+
+EAPI=5
+
+# ebuild generated by hackport 0.3.2.9999
+
+CABAL_FEATURES="bin lib profile haddock hoogle hscolour"
+inherit haskell-cabal
+
+DESCRIPTION="A bioinformatics library"
+HOMEPAGE="http://biohaskell.org/Libraries/Bio"
+SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0/${PV}"
+KEYWORDS="~amd64 ~x86"
+IUSE="+examples test"
+
+RDEPEND=">=dev-haskell/binary-0.4:=[profile?] <dev-haskell/binary-0.8:=[profile?]
+		dev-haskell/mtl:=[profile?]
+		dev-haskell/parallel:=[profile?]
+		dev-haskell/parsec:=[profile?]
+		>=dev-haskell/quickcheck-2:=[profile?]
+		dev-haskell/random:=[profile?]
+		>=dev-haskell/tagsoup-0.8:=[profile?]
+		>=dev-lang/ghc-6.10.4:="
+DEPEND="${RDEPEND}
+		>=dev-haskell/cabal-1.6"
+
+src_prepare() {
+	cabal_chdeps \
+		'binary >=0.4 && <0.5' 'binary >=0.4 && <0.8'
+}
+
+src_configure() {
+	haskell-cabal_src_configure \
+		$(cabal_flag examples examples) \
+		$(cabal_flag test test)
+}
+
+src_test() {
+	dist/build/qc/qc || die
+}
+
+src_install() {
+	haskell-cabal_src_install
+
+	use test && rm "${ED}"/usr/bin/qc
+	# many examples collide with dev-haskell/flower
+	if use examples ; then
+		pushd "${ED}"/usr/bin
+		local example
+		for example in *
+		do
+			mv "${example}" "${PN}-example-${example}"
+		done
+		popd
+	fi
+}
diff --git a/dev-haskell/bio/metadata.xml b/dev-haskell/bio/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>haskell</herd>
+	<maintainer>
+		<email>haskell@gentoo.org</email>
+	</maintainer>
+	<longdescription>
+		This is a collection of data structures and algorithms
+		useful for building bioinformatics-related tools
+		and utilities.
+		
+		Current list of features includes: a Sequence data type supporting
+		protein and nucleotide sequences and conversion between them.  As of version
+		0.4, different kinds of sequence have different types.  Support for quality
+		data, reading and writing Fasta formatted files, reading TwoBit and
+		phd formats, and Roche/454 SFF files.  Rudimentary (i.e. unoptimized) support
+		for doing alignments - including dynamic adjustment of scores based on sequence quality.
+		Also Blast output parsing.  Partly implemented single linkage clustering, and
+		multiple alignment.  Reading Gene Ontology (GO) annotations (GOA) and
+		definitions\/hierarchy.
+		
+		The Darcs repository is at: &lt;http://malde.org/~ketil/biohaskell/biolib&gt;.
+	</longdescription>
+</pkgmetadata>