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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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
The default shared Genome Database location is <code>/project/bio/gmap</code>. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches. | The default shared Genome Database location is <code>/project/bio/gmap</code>. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches. | ||
Revision as of 18:43, 13 July 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).
- 20120703, available on both EL5 and EL6.
- 20120712 (default), available on both EL5 and EL6.
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.
How To Run
The default shared Genome Database location is /project/bio/gmap. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.