Install

Installation

To use Hagfish you'll need:

If on Ubuntu, you can run::

apt-get install samtools python-numpy python-matplotlib

You will also need BAM files, which can be prepared using a read mapper, for example: bowtie). Read more on read mappers and Hagfish here

And obviously, you'll need Hagfish. To download, either clone the github hagfish repository, download the zipfile or tarball.

Ensure the source code is (unpacked in) a convenient location and add it to your path, for example by adding this to your ~/.bashrc:

export PATH=/path/to/hagfish:$PATH

Make sure that you log out and in again or source your .bashrc (. ~/.bashrc).

Hagfish should now be ready to use.