PASA

From UFRC
Revision as of 17:53, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "")
Jump to navigation Jump to search



Description

pasa website  

The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.

Available Versions

  • 20110520

Required Modules

modules documentation

Serial

  • pasa
  • HPC_PASA_BIN - executable directory.
  • HPC_PASA_CONF - config file directory.

How To Run

Tools and variables

  • UNIVECDB environment variable is set to the location of the UniVec database for use by seqclean.

Databases

  • The MySQL server used by PASA has been configured to allow the pasaadmin user to create databases with names that end in _pasa only. So, to run pasa your configuration file such as alignAssembly.config or conf.txt must have MySQL configuration similar to the following entry:
MYSQLDB=test_run_pasa

The example configuration files are located in /apps/pasa/20110520/pasa_conf ($HPC_PASA_CONF) directory.

Web Portal

You can visualize the results of your PASA run by going to the "http://pasa.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$MYSQL_DB" URL where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.