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).
• 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.