Difference between revisions of "Gmap"
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_GMAP_BIN - executable directory. | * HPC_GMAP_BIN - executable directory. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Revision as of 18:32, 10 August 2012
Description
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program
Required Modules
Serial
- gmap
System Variables
- HPC_{{#uppercase:gmap}}_DIR - installation directory
- 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.