@hackage bio0.5.1

biolib - a Haskell library for bioinformatics

This is a collection of data structures and algorithms I've found useful when building various bioinformatics-related tools and utilities.

Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them, quality data, reading and writing FASTA formatted files, reading TwoBit and phd formats, and also FastQ. Rudimentary support for doing alignments

• including dynamic adjustment of scores based on sequence quality - and Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading and writing 454-style SFF sequences, with a bunch of useful (and not-so-useful) operations on them.

To install, you need to acquire a working GHC (possibly other Haskell system). You also need the following external libraries:

QuickCheck - for unit tests ('make test' to run them) binary - mainly for dealing with the TwoBit sequence format tagsoup - for parsing XML output from Blast parsec - for parsing ACE, Bowtie and Soap output

You should be able to get what you need from http://hackage.haskell.org/.

The easiest way these days, is to use 'cabal'. You can get away with

cabal install bio

As an alternative, you can build with 'make', doing either 'make install' if you can sudo, or 'make user_install' if you can not. Of course, the Makefile just proxies for the regular Cabal routine, which will work just as well:

runhaskell Setup configure runhaskell Setup build sudo runhaskell Setup install

(Use --prefix=$HOME and remove the sudo, if you don't want to install as root.)

If that didn't work, mail me at ketil@malde.org, and we'll try to work things out.