Dependancies that must be installed and available in path:
blastall
formatdb

Dependancies distributed with hamster and galaxy hamster
BioPerl
genewise
rungenewise.pm
wisecfg -- directory of configuration files for genewise



QUICKSTART

1. Copy galaxy_hamster files into the directory where you want to
install the program.

2. execute the install.pl script to configure required directories.
Type:

./install.pl

3. Make sure blastall and formatdb are installed on your system,
   and have been configured on your PATH.

4. add ucsb_hamster.xml to Galaxy's tool_conf.xml file.

5. Restart Galaxy


Now, ucsb hamster can be used using HMM's constructed in a Galaxy
history using phytab_hmmbuild.






DETAILED INSTALLATION PROCEDURES:

If for some reason install.pl does not work, first make sure that
you have deleted the PATH variable pointing to any existing galaxy_hamster
installation on your system in the .bashrc file.

If you have deleted this variable and still cannot execute the install script,
you may follow the detailed installation procedure below.

1. Copy galaxy_hamster files into the directory where you want to install
the program.

2. Directory that contains the following scripts must be in the overall
path:
translate.pl
emap2fasta.pl
unbuild.py

You may add the directory into your .bashrc file located in your HOME directory.

For example:
export PATH="/home/galaxy/galaxy-dist/tools/galaxy_hamster:$PATH";

3. Type: source .bashrc to reload your environment variables.

4. In the file run_genewise.pm located in the lib direcotry, you must set the full 
path of the genewise configuration directory. The configurat iondirectory is 
called wisecfg and it is distributed with galaxy_hamster.

5. From here, ensure that blastall and formatdb are installed on your system and
have been configured on your PATH.

6. Add ucsb_hamster.xml to Galaxy's tool_conf.xml file.

7. When installing on an Ubuntu system, the ucsb_hamster.sh script was not finding
translate.pl even though it was in the path. To fix this I (THO) added translate.pl and 
the main hamster script to /usr/local/bin/ with a symbolic link, which seemed to fix 
this problem.

8. Restart Galaxy.