Difference between revisions of "PASA"
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===Databases=== | ===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: | * 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= | + | MYSQLDB=pasa_test_run |
The example configuration files are located in <code>/apps/pasa/20110520/pasa_conf</code> ($HPC_PASA_CONF) directory. | The example configuration files are located in <code>/apps/pasa/20110520/pasa_conf</code> ($HPC_PASA_CONF) directory. | ||
| + | |||
| + | Make sure to name your pasa database as 'pasa_${USER}_$NAME' where '$NAME' is the name you want to give the database and '$USER' is your username. For example a database can be named as 'pasa_jdoe_experiment_1'. | ||
|}} | |}} | ||
===Web Portal=== | ===Web Portal=== | ||
Revision as of 04:51, 3 February 2015
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.
Required Modules
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
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=pasa_test_run
The example configuration files are located in /apps/pasa/20110520/pasa_conf ($HPC_PASA_CONF) directory.
Make sure to name your pasa database as 'pasa_${USER}_$NAME' where '$NAME' is the name you want to give the database and '$USER' is your username. For example a database can be named as 'pasa_jdoe_experiment_1'.
Web Portal
You can visualize the results of your PASA run by going to "http://pasa2.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$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.