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biohazard

This is a library for Bioinformatics, mostly centered on the BAM file format for Next Generation Sequencing data. A number of tools built on top of it can be found in the biohazard-tools repository at https://bitbucket.org/ustenzel/biohazard-tools.

Installation

Biohazard uses Cabal, the standard installation mechanism for Haskell.
To install, follow these steps:

  • install GHC (see http://haskell.org/ghc, version 8.4.4 is recommended) and cabal-install (see http://haskell.org/cabal, version 2.4.0.0 is recommended),
  • cabal update (takes a while to download the current package list),
  • git clone https://ustenzel@bitbucket.org/ustenzel/biohazard.git
  • cabal install biohazard/ (takes even longer).

Sometimes, repeated installations and re-installations can result in a thoroughly unusable state of the Cabal package collection. If you get error messages that just don't make sense anymore, please refer to http://www.vex.net/~trebla/haskell/sicp.xhtml; among other useful things, it tells you how to wipe a package database without causing more destruction.