Difference between revisions of "PASA"
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
* HPC_PASA_BIN - executable directory. | * HPC_PASA_BIN - executable directory. | ||
| + | * HPC_PASA_CONF - config file directory. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
===Tools and variables=== | ===Tools and variables=== | ||
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* 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=test_run_pasa | MYSQLDB=test_run_pasa | ||
| + | |||
| + | The example configuration files are located in <code>/apps/pasa/20110520/pasa_conf</code> ($HPC_PASA_CONF) directory. | ||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 17:04, 17 February 2012
Description
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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.
Template:App Location
Available Versions
- 20110520
Running the application using 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.