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PASA

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.

  • PASAHOME - base directory * UNIVECDB - UniVec database location

Environment Modules

Run module spider pasa to find out what environment modules are available for this application.

Environment Variables

  • HPC_PASA_DIR - installation directory
  • HPC_PASA_BIN - executable directory
  • HPC_PASA_CONF - config file directory

Additional Usage Information

Tools and variables

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

Databases

Tip

We have a single DB server that supports all applications that make use of databases. Use SLURM Job Arrays and throttle your jobs to at most 10 active tasks at a time to avoid overwhelming it.

The MySQL server used by PASA has been configured to allow the pasaadmin user to create databases with names in the form of "pasa_${USER}_".

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_jdoe_run1

The example configuration files are located in $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.

Please contact us if you would like to prevent automatic removal of old PASA databases. We may remove all databases over six months old.

Use helper tools we created for managing PASA databases. The following tools are available:

  • rc_list_pasa_databases
    List all databases named pasa_% on the server

  • rc_create_pasa_db NAME
    Create an empty database with name NAME. Name your databases as shown above

  • rc_export_pasa_db NAME
    Save your PASA database named NAME to a file named NAME.sql in the current working directory.
    Use this to backup databases, so they don’t get lost in a cleanup if you may need them later.

  • rc_import_pasa_db NAME.sql
    Create a database called NAME and import structure and data from an SQL file called NAME.sql

  • rc_remove_pasa_db
    Remove a database you no longer need from the server.

Web Portal

Note

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

Categories

biology, genomics, ngs