dev-haskell / bio

A bioinformatics library

Official package sites : http://biohaskell.org/Libraries/Bio ·

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>.

v0.5.3-r2 :: 0/0.5.3 :: gentoo

Modified
License
LGPL-2.1
Keywords
~amd64 ~x86
USE flags
doc examples hscolour profile test

General

doc
Add extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
examples
Install examples, usually source code
hscolour
Include coloured haskell sources to generated documentation (dev-haskell/hscolour)
profile
Add support for software performance analysis (will likely vary from ebuild to ebuild)
test
Enable dependencies and/or preparations necessary to run tests (usually controlled by FEATURES=test but can be toggled independently)

dev-haskell / binary : Binary serialisation for Haskell values using lazy ByteStrings

dev-haskell / cabal : A framework for packaging Haskell software

dev-haskell / haddock : A documentation-generation tool for Haskell libraries

dev-haskell / hscolour : Colourise Haskell code

dev-haskell / mtl : Monad classes, using functional dependencies

dev-haskell / old-time : Time library

dev-haskell / parallel : Parallel programming library

dev-haskell / parsec : Monadic parser combinators

dev-haskell / quickcheck : Automatic testing of Haskell programs

dev-haskell / random : random number library

dev-haskell / tagsoup : Parsing and extracting information from (possibly malformed) HTML/XML documents

dev-lang / ghc : The Glasgow Haskell Compiler

dev-haskell / binary : Binary serialisation for Haskell values using lazy ByteStrings

dev-haskell / mtl : Monad classes, using functional dependencies

dev-haskell / old-time : Time library

dev-haskell / parallel : Parallel programming library

dev-haskell / parsec : Monadic parser combinators

dev-haskell / quickcheck : Automatic testing of Haskell programs

dev-haskell / random : random number library

dev-haskell / tagsoup : Parsing and extracting information from (possibly malformed) HTML/XML documents

dev-lang / ghc : The Glasgow Haskell Compiler

Repository mirror & CI · gentoo
Merge updates from master
Michał Górny · gentoo
*/*: [QA] Fix trivial cases of MissingTestRestrict
The result was achieved via the following pipeline: pkgcheck scan -c RestrictTestCheck -R FormatReporter \ --format '{category}/{package}/{package}-{version}.ebuild' | xargs -n32 grep -L RESTRICT | xargs -n32 sed -i -e '/^IUSE=.*test/aRESTRICT="!test? ( test )"' The resulting metadata was compared before and after the change. Few Go ebuilds had to be fixed manually due to implicit RESTRICT=strip added by the eclass. Two ebuilds have to be fixed because of multiline IUSE. Suggested-by: Robin H. Johnson <robbat2@gentoo.org> Closes: https://github.com/gentoo/gentoo/pull/13942 Signed-off-by: Michał Górny <mgorny@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Michał Górny · gentoo
*/*: Inline mirror://hackage and update URIs
This change inlines mirror://hackage in all ebuilds, and updates URIs to the modern form (old URIs redirect to that). The change has been made using the following command: find -name '*.ebuild' -exec sed -r -i \ -e 's@mirror://hackage/@https://hackage.haskell.org/@g' \ -e 's@https://hackage.haskell.org/packages/archive/([^/]*)/([^/]*)/@https://hackage.haskell.org/package/\1-\2/@g' \ -e '/hackage\.haskell\.org/s@\$\{PN}-\$\{PV}@${P}@g' \ -e '/hackage\.haskell\.org/s@\$\{MY_PN}-\$\{PV}@${MY_P}@g' \ -e '/hackage\.haskell\.org/s@\$\{PN}-\$\{MY_PV}@${MY_P}@g' \ {} + Signed-off-by: Michał Górny <mgorny@gentoo.org>
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Sergei Trofimovich · gentoo
dev-haskell/bio: drop old
Package-Manager: portage-2.3.0_rc1
Sergei Trofimovich · gentoo
dev-haskell/bio: allow binary-0.8, add missing depend, bug #585318
Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/585318 Package-Manager: portage-2.3.0_rc1
Sergei Trofimovich · gentoo
dev-haskell/bio: drop old
Package-Manager: portage-2.2.28
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed