@hackage bio0.4

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. 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.

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

QuickCheck - for unit tests binary - mainly for dealing with the TwoBit sequence format tagsoup - for parsing XML output from Blast

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

You can then 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.