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Load the software

When running module spider orthomcl on a dev-node, you will see the following:

----------
OrthoMCL:
----------
    Description:
      OrthoMCL is a genome-scale algorithm for grouping orthologous protein
      sequences.

     Versions:
        OrthoMCL/2.0.9-custom-Perl-5.24.0
        OrthoMCL/2.0.9-Perl-5.24.0

They are the same version of OrthoMCL, except that the custom one has fixed a possible error due to sequence identifier. See the issue reported in GitHub.

Since OrthoMCL uses BLAST, it needs to be loaded as well. An example of loading OrthoMCL would be

module purge
module load icc/2016.3.210-GCC-5.4.0-2.26  impi/5.1.3.181
module load OrthoMCL/2.0.9-custom-Perl-5.24.0
module load BLAST/2.2.26-Linux_x86_64

The next thing you need to do is to request and set up your MySQL configuration file, see https://docs.icer.msu.edu/MySQL_configuration/

After you have your config file (say orthomcl.config) ready, you need to run orthomclInstallSchema to install the required schema into the database:

orthomclInstallSchema orthomcl.config install_schema.log

For the rest of your analysis steps, please read http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt