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