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MetAMOS is a Python-based software package that provides a framework for genome assembly and analysis.  It provides a flexible pipeline for calling underlying third-party programs for pre-processing, genome assembly, classification, annotation and other common tasks.  As such, there are many optional components. If one of the potential dependencies has not been installed, please contact WestGrid support to discuss whether it can be installed.

Caution:  Since the hardware requirements (for example memory usage) and degree of parallelization can vary greatly from one pipeline step to the next, use of this kind of software in a shared batch environment is problematic.  It may actually be better to run some of the underlying programs separately, rather than in an overly-automated pipeline.

Running MetAMOS on Breezy

To try MetAMOS on Breezy, include the following initialization steps in your job script before calling MetAMOS commands:

module load python
export PATH=/global/software/metamos/metAMOS_1.1:$PATH

Additional initialization may be required, depending on which underlying assemblers or other third-party programs you require to complete your analysis.

For More Information

2015-01-06 - Created MetAMOS page.

System Breezy
Version 1.1