Difference between revisions of "PASA"

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===Web Portal===
 
===Web Portal===
You can visualize the results of your PASA run by going to the "http://pasa2.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. Pasa 1.5 URIs can be reached at http://pasa.hpc.ufl.edu.
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You can visualize the results of your PASA run by going to "http://pasa2.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$MYSQL_DB" URI where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.  
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Note: Pasa2 web interface no longer has an administrative page. Go directly to status_report.cgi.
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Pasa 1.5 URIs can be reached at http://pasa.hpc.ufl.edu.
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}

Revision as of 17:25, 24 September 2013

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.

Required Modules

modules documentation

Serial

  • pasa

System Variables

  • HPC_{{#uppercase:pasa}}_DIR - installation directory
  • HPC_PASA_BIN - executable directory.
  • HPC_PASA_CONF - config file directory.

Additional Information

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 "http://pasa2.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$MYSQL_DB" URI where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.

Note: Pasa2 web interface no longer has an administrative page. Go directly to status_report.cgi.

Pasa 1.5 URIs can be reached at http://pasa.hpc.ufl.edu.