Genomics Software Repository on Iceberg, the High Performance Computing Cluster at the University of Sheffield

To develop and support the analytical infrastructure of the Molecular Ecology Group at the University of Sheffield, a Genomics Software Repository has been established.

The Genomics Software Repository is a shared folder on Iceberg, the High Performance Computing Cluster at the University of Sheffield. The aim of the Genomics Software Repository is to facilitate NGS data and population genetic/genomic analyses using the Iceberg platform. The shared folder contains installed and enabled NGS and population genetic/genomic softwares (e.g. BEAST, Colony, STACKS, GATK). Softwares can be run by including a directory pathway to the software in the job submission script. The advantage is it removes the necessity for the user to install softwares to their personal folder. Additionally the shared folder contains example job submission scripts for various analyses that can be copied and modified by the user and some tutorials for how to run softwares.

The Genomics Software Repository shared folder is accessible from this directory:  /usr/local/extras/Genomics

Example job submission scripts are available to copy to your user profile from this directory:

/usr/local/extras/Genomics/submit_scripts

All Iceberg users have access to Genomics Software Repository; however, to access you must be on a worker node (and not the head node).

For more information and a list of installed softwares, access the Genomics Software Repository website from following Genomics link at:

http://www.shef.ac.uk/molecol/software/

We’re launching the Genomics Software Repository and website today to coincide with the final session of the High Performance Computing Course at APS that is supporting training to access these communal resources for NGS and population genetic/genomic analyses.

Best of luck with your future research!

Caitriona McInerney and Victor Soria-Carrasco

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