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Load the software

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

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OrthoMCL:
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    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

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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:

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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