README

Welcome to TE-Tracker, a program dedicated to the de-novo discovery of transposition events.

For installation, please use the command

./install.pl

This will install a standalone version of TE-Tracker in the current directory, downloading all necessary tools and setting the path for them.
The three modules (eris.pl, leto.pl, metis.pl) need to be called sequentially to prepare the BAMs and call transposition events.
You can call the three modules directly but it is recommended to use the tetracker executable (tetracker eris, tetracker leto, tetracker metis).

Manual.pdf contains a quick-start guide that will allow the user to rapidly generate datasets comparable to those presented in the original article.

Once TE-Tracker is installed, the 'man' subcommand will open a manual for each of the programs (tetracker man, tetracker eris man, etc.).


TROUBLESHOOTING
===============


TE-Tracker has not been extensively tested on a different environment than the one it was written in. We cannot guarantee that all errors are described here.
If you experience any errors not reported below, please contact ag15@sanger.ac.uk.

- After installation, you might get a "permission denied" error when executing TE-Tracker. This was found to occur when perl is installed in a non-standard location. Please make sure that /usr/bin/perl exists, or replace the shebang line (#!) in tetracker, eris.pl, leto.pl, metis.pl, by the path to your perl executable.
- A "Could not create the Java virtual machine" can be thrown by Java. Please make sure that the path to a working java executable is in your PATH and that Java is correctly configured on your machine.