Difference between revisions of "PASA"
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
===Tools and variables=== | ===Tools and variables=== | ||
| − | * <code> | + | * <code>UNIVECDB</code> environment variable is set to the location of the UniVec database for use by seqclean. |
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 18:41, 10 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.
How To Run
Tools and variables
UNIVECDBenvironment variable is set to the location of the UniVec database for use by seqclean.