Difference between revisions of "Stacks"
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To run stacks with database export: | To run stacks with database export: | ||
| − | * Log into a | + | * Log into a dev node and load the stacks module: |
* Create a database with a name that starts with <code>"stacks_${USER}_" or "radtags_${USER}_" using the 'hpc_create_stacks_db' script | * Create a database with a name that starts with <code>"stacks_${USER}_" or "radtags_${USER}_" using the 'hpc_create_stacks_db' script | ||
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* Log out of the dev node. | * Log out of the dev node. | ||
* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags". | * Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags". | ||
| − | * Browse to [http://stacks. | + | * Browse to [http://stacks.rc.ufl.edu stacks.rc.ufl.edu] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows: |
| − | <nowiki>http://stacks. | + | <nowiki>http://stacks.rc.ufl.edu/stacks/index.php?db=DATABASE</nowiki> |
| − | Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to [http://stacks. | + | 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/index.php?db=stacks_tut http://stacks.rc.ufl.edu/index.php?db=stacks_tut] for the output of a [http://creskolab.uoregon.edu/stacks/tut.php#pipe Stacks Tutorial]. |
|}} | |}} | ||
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 16:15, 3 October 2014
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
Serial
- stacks
System Variables
- HPC_{{#uppercase:stacks}}_DIR - installation directory
Additional Information
The command line pipeline is available via the "stacks" module.
The web interface that can be used for visualizing genetic maps and correcting the analysis is being installed and tested as of Aug 21st, 2012.
To run stacks with database export:
- Log into a dev node and load the stacks module:
- Create a database with a name that starts with
"stacks_${USER}_" or "radtags_${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 test1_radtags".
- Browse to stacks.rc.ufl.edu and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
http://stacks.rc.ufl.edu/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/index.php?db=stacks_tut for the output of a Stacks Tutorial.