From 8376ef56580626e9c0f796d5b85b53a0a1c7d5f5 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 14 Jul 2018 21:03:06 +0100 Subject: gentoo resync : 14.07.2018 --- dev-haskell/bio/Manifest | 4 ++ dev-haskell/bio/bio-0.5.3-r2.ebuild | 63 ++++++++++++++++++++++++++ dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch | 7 +++ dev-haskell/bio/metadata.xml | 25 ++++++++++ 4 files changed, 99 insertions(+) create mode 100644 dev-haskell/bio/Manifest create mode 100644 dev-haskell/bio/bio-0.5.3-r2.ebuild create mode 100644 dev-haskell/bio/files/bio-0.5.3-ghc-7.10.patch create mode 100644 dev-haskell/bio/metadata.xml (limited to 'dev-haskell/bio') diff --git a/dev-haskell/bio/Manifest b/dev-haskell/bio/Manifest new file mode 100644 index 000000000000..09849c9c8fd8 --- /dev/null +++ b/dev-haskell/bio/Manifest @@ -0,0 +1,4 @@ +AUX bio-0.5.3-ghc-7.10.patch 266 BLAKE2B 2db06eaf40ef90741aca5c329e096a82f259c5c068728338d798ba083ab7cd194f95cb54d0b2eee1257b15b8cce534a270adfd4b01b21ecab7245eb88b5b1bb5 SHA512 58efe74d17f2233f43c43d56eaabb849bc7753e27b3499544856036984504add5a50f4d6e1cf43af64a19695c1ef44cdd82514ce5126d50815b659e20bd93785 +DIST bio-0.5.3.tar.gz 103707 BLAKE2B 31c9e354ba33f20d6129a20d6272063498bfd4b4ea2cba9eddab8ede62ee894659eb5e6383ef022f5e003deab8bb3c92a98bcadae44db22e7b0346471cad5e4d SHA512 fbe09240a600abbcac952f52f05f28f9b305a1ae3def8b4144bd73bdb160acfbe5457086ef829057d5a73df1df5061668487b2ca5621df73628c8c4990b6b544 +EBUILD bio-0.5.3-r2.ebuild 1404 BLAKE2B 434ee9037af79c29b9d4097a0eb34813187bd111e17619d4527959fc0fe4b4ff6008480d46801963c12cfc4db71a81fc9b8454f174f6cef8062e04ceb9f0a45f SHA512 14e47edc973b6fec1b552158be098e7349e35d9ed9285a3cec7d9a3e207bddf8c50adb9ce27e66330d04119adcd10f1045ae961787184e8678db71b83e757933 +MISC metadata.xml 1145 BLAKE2B 1b90a811913c7c6247ca1e2237a8d0ea8e0bd56f7e3310a5e61df90d6dadc365ed4a5c58829a94efe61f88c57270e7c715989f5b0ff02ad75395703e2d7bd596 SHA512 c91ebcc3b83ab7d9bbcaee0cff08cf212b3d77b1d2a34c70308d7bb3ff47f898668c1cb13c2e761ce25653bf167bce55fa9dd848d52e6ffd8e93021e173e8e7f 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 @@ + + + + + haskell@gentoo.org + Gentoo Haskell + + + 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: <http://malde.org/~ketil/biohaskell/biolib>. + + -- cgit v1.2.3