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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


  • pasa


  • gcc/5.2.0
  • pasa

See 'module spider pasa' and check the version you want to run with module spider pasa/$version to know what modules to load.

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.


we have a single DB server that supports all applications that make use of databases. Use SLURM Job Arrays and throttle you 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:


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.

Web Portal

You can visualize the results of your PASA run by going to "$MYSQL_DB" URI where "$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