Usage

Note

Only SQLite is supported as an OrthoMCL database out of the box at this time unless you attempt to stand up your own MariaDB database in another job using a container on your own.

Configuration¶

The $HPC_ORTHOMCL_CONF/orthomcl.config file provides a template for configuring an OrthoMCL SQLite database. Copy it to your working directory with

$ cp $HPC_ORTHOMCL_CONF/orthomcl.config .

The $HPC_ORTHOMCL_CONF/orthomcl.config.sql file provides a template for configuring an OrthoMCL MySQL database. Copy it to your working directory with

$ cp $HPC_ORTHOMCL_CONF/orthomcl.config.sql .

Don't forget to create the schema with the following before creating a database:

orthomclInstallSchema orthomcl.config

A wrapper script orthomcl_wrapper_SQLITE that creates a suitable orthomcl.config file and automates much of the pipeline is provided:

$ orthomcl_wrapper_SQLITE -p compliantFASTA -u 2 -s 100
-p path to folder with input fasta files 
-u position of unique IDs in fasta headers
-s number of parallel blast jobs to run in a slurm array.

The wrapper script writes a run_split_blast_array.sh script that can be modified to resubmit blast jobs if necessary, and a finish.orthomcl.sh script to be run after all blast jobs complete.

Documentation for SQLite support can be found on the OrthoMCL GitHub.
OrthoMCL User Guide can be found at Wiley Online Library. The original publications that describe the functionality of the software are 10.1101/gr.1224503 and 10.1093/nar/gkj123.