Gmap

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.

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.