What is GARLI, and how can I use it on Quarry?

About GARLI

The GARLI package conducts phylogenetic searches on aligned sequences using maximum likelihood criteria. It supports codon- and amino-acid-based models in addition to standard nucleotide models. The current version of GARLI on Quarry is 0.96b8.

For information about GARLI packages, see the GARLI home page, GARLI FAQ, and GARLI manual (also available in PDF format). At Indiana University, an example data set is available on Quarry at /N/soft/linux-rhel4-x86_64/Garli/example.

Using GARLI on Quarry

At Indiana University, GARLI is available on Quarry. Accounts on Quarry are available to all IU students, faculty, and staff, as well as affiliated researchers. Instructional use is limited to courses approved by the Director for Research Technologies. If you use Quarry, you need to know the Quarry usage policies.

To use GARLI on Quarry:

1. Request a Quarry account
2. Set up SoftEnv and submit jobs
3. Write a garli.conf file
4. Using the Garlijob script to submit a batch job

Request a Quarry account

To request a Quarry account, use the Account Management System (AMS); see At IU, if I already have some computing accounts, how do I get others? For more, see Getting started on Quarry.

Set up SoftEnv and submit jobs

1. To set up your SoftEnv, edit your .soft file to add the line +garli and execute the resoft command.
   
   
2. Create a working directory that contains all the data files (in .nex format ) and a parameter file named garli.conf. (See Write a garli.conf file below.)
   
   
3. If your job will run for fewer than 20 minutes, call garli in the directory where your input files are.

If your job will take longer than 20 minutes, use the Garlijob script (see Using the Garlijob script to submit a batch job below.)

Output that GARLI generates will be in the same directory as your input files. Note that if you did not pass a config filename on the command line, the program will look in the current directory for a file named garli.conf.

Write a garli.conf file

All the parameters that GARLI takes are stored by default in garli.conf. To learn how to write your garli.conf file, see the GARLI manual (PDF) or the GARLI Configuration Settings page.

Using the Garlijob script to submit a batch job

If your job will require more than 20 minutes to finish, you can use the Garlijob script to submit a batch job. This script will set up the working environment, write a PBS script, and submit this PBS script to run as a batch job.

To learn how to use Garlijob, enter garlijob at the prompt. You will see the following information:

The first option, configure_file_of_Garli, is necessary; for more information, see the section above about the garli.conf file.

Also see:

• Bioinformatics support