Bioinformatics software at IU

UITS provides bioinformatics software on the Karst and Mason research computing clusters.

To determine which bioinformatics packages are available on either system, from the command line, enter module avail. On Karst, bioinformatics packages are listed in the output under /N/soft/rhel6/modules/quarry/LIFE-SCIENCES. On Mason, they are listed in the output under /N/soft/rhel6/modules/mason/LIFE-SCIENCES.

On the research computing resources at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.

To add any of these packages to your user environment on Karst or Mason, use the module load command. For example, on the command line, enter the following (replace package with the appropriate module name and version with the desired version number):

  module load package/version

For some packages (or particular versions), you must add one or more prerequisite packages before you can load the desired module. For example, on Karst, the default version of mothur (a bioinformatics tool for analyzing 16S rRNA gene sequences) is the MPI version. Consequently, before you can add the default version of mothur, you must add the prerequisite GNU OpenMPI libraries:

  [bobafett@h2 ~]$ module load openmpi/gnu
  OpenMPI libraries (GNU) version 1.8.4 loaded.

Once the prerequisite module is loaded, you can load the default version of mothur without including the version information:

  [bobafett@h2 ~]$ module load mothur 
  Mothur (MPI) version 1.34.2 loaded.

To use the non-default, serial version of mothur instead, you must specify both the module name and the appropriate version number in your module load command:

  [jangfett@h2 ~]$ module load mothur/1.34.2
  Mothur version 1.34.2 loaded.

To make permanent changes to your environment, edit your ~/.modules file. For more, see In Modules, how do I save my environment with a .modules file?

If you need help or have questions about bioinformatics software on Karst, email the UITS Scientific Applications and Performance Tuning (SciAPT) team. To request software for general use on Karst, submit the Software Request Form.

Software on Mason is supported by The National Center for Genome Analysis Support (NCGAS). If you need help or have questions about bioinformatics software on Mason, contact NCGAS. To request software on Mason, use the NCGAS Software Request Form. For more, see Software supported by NCGAS and At IU, what is the policy about installing software on Mason?

For more about the Modules package, see the module manual page and the modulefile manual page. Additionally, see On Big Red II, Karst, and Mason at IU, how do I use Modules to manage my software environment?

This is document alei in the Knowledge Base.
Last modified on 2015-06-23.

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