PASA: Difference between revisions
Moskalenko (talk | contribs) m Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==" |
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
{{#if: {{#var: policy}}|==Usage | {{#if: {{#var: policy}}|==Usage Policy== | ||
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Revision as of 16:32, 10 August 2012
Description
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
Execution Environment and Modules
To use pasa with the environment modules system at HPC the following commands are available:
Get module information for pasa:
$module spider pasa
Load the default application module:
$module load pasa
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_PASA_DIR - directory where pasa is located.
- HPC_PASA_BIN - executable directory.
- HPC_PASA_CONF - config file directory.
How To Run
Tools and variables
UNIVECDBenvironment variable is set to the location of the UniVec database for use by seqclean.
Databases
- The MySQL server used by PASA has been configured to allow the pasaadmin user to create databases with names that end in _pasa only. So, to run pasa your configuration file such as alignAssembly.config or conf.txt must have MySQL configuration similar to the following entry:
MYSQLDB=test_run_pasa
The example configuration files are located in /apps/pasa/20110520/pasa_conf ($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.