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.