Accessing Software via the Modules Command

When a PBS script is created, multiple software programs are typically utilized. Many programs, including ones that represent software ranging from DNA sequencing to others that isolate/cross reference genetic patterns, can be accessed using the module command. To view the available modules, enter the following command:

$ module avail

Once the list populates, determine which module(s) you require to perform your analysis:  

abyss/1.2.7                        mergemap/20130627
abyss/1.3.2                        metavelvet/1.2.01
addscores/bbfea952f091             mira/3.4.0
allpaths/2.2                       misa/2010-09-27
allpathslg/38469                   mosaik/1.1.0021(default)
amos/3.0.1                         mosaik/2.1.33
amos/3.1.0                         mothur/1.23.1
ampliconnoise/1.25                 mummer/3.22
augustus/2.5.5                     ncbi-blast+/2.2.25
augustus/2.6.1                     ncbi-blast+/2.2 

To incorporate modules into your script, enter (for example) the following command(s):

module load abyss  
module load augustus
module load mummer

Note: The newest versions of modules automatically load; however, older versions can be accessed by adding the file extension (e.g., module load abyss/1.2.7).

Commonly Used Module Commands:

$ module avail Lists all module packages available                                         
$ module load module_name Adds module to a script or session
$ module whatis module_name Provides module description
$ module unload Removes modules from script or session
$ module list Lists modules already loaded