Difference between revisions of "PASA"
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Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:Genomics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the v...") |
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{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
{{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. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
===Tools and variables=== | ===Tools and variables=== | ||
Revision as of 18:40, 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
$UNIVECDBvariable is set to the location of the UniVec database used by seqclean.