reinit the tree, so we can have metadata

4 files changed, 101 insertions, 0 deletions

diff --git a/dev-haskell/bio/Manifest b/dev-haskell/bio/Manifest
new file mode 100644
index 000000000000..4fc698f29f4c
--- /dev/null
+++ b/dev-haskell/bio/Manifest
@@ -0,0 +1,6 @@
+AUX bio-0.5.3-ghc-7.10.patch 266 SHA256 fb77daf3d9c8e3e6b4fd7bf49e83e2233b49919dbfc5f3fb2cb2c11cc4579201 SHA512 58efe74d17f2233f43c43d56eaabb849bc7753e27b3499544856036984504add5a50f4d6e1cf43af64a19695c1ef44cdd82514ce5126d50815b659e20bd93785 WHIRLPOOL 3a52c831f8478a5cbd9e469b9c356199966b31b84d2fc10d00338f669f017b079ee6fa8052ac77ca229b0750393f98261ad00e4e31c0820e898c417f9a91276d
+DIST bio-0.5.3.tar.gz 103707 SHA256 42c8f9b83fea6bf51356afe1251910ba4421e0af0bb4f26431eaf385971d7eed SHA512 fbe09240a600abbcac952f52f05f28f9b305a1ae3def8b4144bd73bdb160acfbe5457086ef829057d5a73df1df5061668487b2ca5621df73628c8c4990b6b544 WHIRLPOOL 84d057c68b0fbf899594470e171f883b92def29f0f7f607b08d0d419dd01c5f2e0f6054f93387c32b6b7ffdd1ceb6e84ef6b8cfe5faaee1f89c2e8b10837dcb8
+EBUILD bio-0.5.3-r2.ebuild 1404 SHA256 83b07623872fdb45c5377ab322b5daaa376abec46b68b89a7eda703e84ff5247 SHA512 14e47edc973b6fec1b552158be098e7349e35d9ed9285a3cec7d9a3e207bddf8c50adb9ce27e66330d04119adcd10f1045ae961787184e8678db71b83e757933 WHIRLPOOL 671fd2ed961b5fe22053604b3fea2b5406571aee967dfc3e2489bd9378f8bb3c6ae997a1bc1011601eb99cb40838935c9d3610f5f4b97dda01fbb2234575c7e3
+MISC ChangeLog 3013 SHA256 650e0356356b8300448ec574d71c1a4f9aa9774c61c354e8db0c34787bfad2fa SHA512 00283fa144fddf08184083536a8ca53f961d15e3e1cca5bfb3387f9dc4837b2e16c5ab48649ad251ced7cf2633602db726408ba6b5a173f17243dd022a7ec198 WHIRLPOOL d7650b90a1264bb1cec15e158ba1f30ce6524aa3f965ddeaf864cb0deacec7ec3dcbe4f4c224bbe923c7273bae2552749c959db6552a700385d872b073a49b5e
+MISC ChangeLog-2015 790 SHA256 1505c7793371c15fa205df2b7dcb948c66ac0410ca0fe4660ce137269063a54b SHA512 c5f02d9f7edd6cda75f6132000d26cda993f3a4738b901fbc284ee004d974faebe239d97bdd2ddc39fda949fd9f464e472d8bead8dc4df40dd91cf7664190ea6 WHIRLPOOL 63ebe6e803fe40c4adf20b3b7b0a1a3f0db33885893a0eeb5afb16d87adbafd3c903d4ccd22384a39db38838eff514c7b6d7788a4f07e163381d4e472fb3b0c5
+MISC metadata.xml 1145 SHA256 1a71793e89f4909f773603e3b9346b8eb8a92b410a299d3b41debfcec746fc81 SHA512 c91ebcc3b83ab7d9bbcaee0cff08cf212b3d77b1d2a34c70308d7bb3ff47f898668c1cb13c2e761ce25653bf167bce55fa9dd848d52e6ffd8e93021e173e8e7f WHIRLPOOL af35ca4ceb006ca7f47e33a5657618ccbe97a0afa5c55c552572cc13ee331a42308222a820f0f779fc03ec917f10aa3d91749a7ae845db53b2be48023c656bab
diff --git a/dev-haskell/bio/bio-0.5.3-r2.ebuild b/dev-haskell/bio/bio-0.5.3-r2.ebuild
new file mode 100644
index 000000000000..c2d94eaad256
--- /dev/null
+++ b/dev-haskell/bio/bio-0.5.3-r2.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+# ebuild generated by hackport 0.3.2.9999
+
+CABAL_FEATURES="bin lib profile haddock hoogle hscolour"
+inherit eutils 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/mtl:=[profile?]
+		dev-haskell/old-time:=[profile?]
+		dev-haskell/parallel:=[profile?]
+		dev-haskell/parsec:=[profile?]
+		>=dev-haskell/quickcheck-2:2=[profile?]
+		dev-haskell/random:=[profile?]
+		>=dev-haskell/tagsoup-0.8:=[profile?]
+		>=dev-lang/ghc-6.10.4:="
+DEPEND="${RDEPEND}
+		>=dev-haskell/cabal-1.6"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-ghc-7.10.patch
+
+	cabal_chdeps \
+		'binary >=0.4 && <0.5' 'binary >=0.4'
+}
+
+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/files/bio-0.5.3-ghc-7.10.patch b/dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch
new file mode 100644
index 000000000000..d570d22917a7
--- /dev/null
+++ b/dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch
@@ -0,0 +1,7 @@
+diff --git a/Bio/Alignment/Bowtie.hs b/Bio/Alignment/Bowtie.hs
+index 883b057..3e58f0e 100644
+--- a/Bio/Alignment/Bowtie.hs
++++ b/Bio/Alignment/Bowtie.hs
+@@ -1 +1,2 @@
++{-# LANGUAGE FlexibleContexts #-}
+ {-| This module provides a data type to represent an alignment
diff --git a/dev-haskell/bio/metadata.xml b/dev-haskell/bio/metadata.xml
new file mode 100644
index 000000000000..8927e5f99073
--- /dev/null
+++ b/dev-haskell/bio/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>haskell@gentoo.org</email>
+		<name>Gentoo Haskell</name>
+	</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>