Stacks

Description

Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

Required Modules

modules documentation

Serial

stacks

System Variables

HPC_{{#uppercase:stacks}}_DIR - installation directory

Additional Information

The command line pipeline is available via the "stacks" environment module.

Note: research databases older than 3 months are not guaranteed to be retained on the research database server. Please open a Support Request if you need to retain the data for a longer period of time.

Running Stacks at UFRC

Log into a dev node and load the stacks module:
Create a database with a name that starts with "stacks_${USER}_" using the 'hpc_create_stacks_db' script

For example:

hpc_create_stacks_db "stacks_${USER}_mytest1"

The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like

hpc_create_stacks_db stacks_jdoe_project21

The script will produce an error and quit if the database already exists.
Use the 'hpc_list_stacks_databases [keyword]' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name.
For example:

hpc_list_stacks_databases test

To delete a stacks database use the 'hpc_remove_stacks_database [database]' command and provide the name of the database you want to delete as an argument.

Log out of the dev node.
Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B stacks_${USER}_test1".
Find the stacks version you ran and Browse to http://stacks.rc.ufl.edu/$version/stacks e.g.  http://stacks.rc.ufl.edu/1.24/stacks and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:

http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=DATABASE

Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to http://stacks.rc.ufl.edu/1.24/stacks/index.php?db=stacks_tut for the output of a Stacks Tutorial.