Difference between revisions of "Gmap"

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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_GMAP_BIN - executable directory.
 
* HPC_GMAP_BIN - executable directory.
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'''Note: perl/5.14.1 and samtools/0.1.18" modules are automatically loaded for GMAP/GSNAP 20120323.
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}

Revision as of 14:01, 29 March 2012

Description

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GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program Template:App Location

Available versions

  • 20070928 (used by PASA).
  • 20120111.
  • 20120323 (default).

Running the application using modules

To use gmap with the environment modules system at HPC the following commands are available:

Get module information for gmap:

$module spider gmap

Load the default application module:

$module load gmap

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_GMAP_DIR - directory where gmap is located.
  • HPC_GMAP_BIN - executable directory.

Note: perl/5.14.1 and samtools/0.1.18" modules are automatically loaded for GMAP/GSNAP 20120323.