Difference between revisions of "Gmap"
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'''Note: perl/5.14.1 and samtools/0.1.18" modules are automatically loaded for GMAP/GSNAP 20120323. | '''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== | ||
| − | + | 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. | |
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Revision as of 19:09, 30 May 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.
- 20120427 (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.
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.