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Overview

OrthoMCL is a program that aids in the identification of orthologs.  The OrthoMCL tool uses NCBI BLAST and the MCL application in conjunction with a relational database (MySQL).  OrthoMCL version 2.0.2 is available on the HPCC and can be loaded as a module.

However, because of the relational database requirement, you may contact John Johnston to setup a database for your runs. This tutorial briefly describes how to obtain access to the program, and how to use configuration files provided for accessing the database.

Database Access

Before beginning your HPCC runs, you will need to email John Johnston a database creation request.  A database server (viking.plantbiology.msu.edu) is available which hosts the MySQL server that will serve your database.  The viking.plantbiology.msu.edu server (located in PLB) is accessible from all compute nodes within the HPCC cluster, but requires that each user have a username and password attached to a specific database instance.  To allow this, a database must be created for you, as well as a MySQL user account.  This information will be provided to you in the form of a configuration file by the person who sets up your database.  This file can then be passed as a command-line argument to relevant scripts comprising the OrthoMCL application, to permit database connections

Configuration File

The following is an example of the configuration file you will receive:

 

dbVendor=mysql
dbConnectString=dbi:mysql:someUserdb:viking.plantbiology.msu.edu:3306
dbLogin=someUser
dbPassword=somePassword
# DO NOT CHANGE ANYTHING ABOVE THIS LINE UNLESS YOU KNOW WHAT YOU'RE DOING
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5
oracleIndexTblSpc=NONE

 

Command Example

A typical run that would require the database configuration file might look something like the following:

 

orthomclPairs orthomcl.config log_file cleanup=[yes|no|only|all] <startAfter=TAG>

 

In the example above, the file "orthomcl.config" is the name of the configuration/connection file (provided by the HPCC) that you want to use for your run.

Purging the Database Between Runs

Once your run is completed, you will need to purge the database of its contents prior to beginning new runs using the same database.  To have this performed, please contact John Johnston.  

To facilitate multiple concurrent, or faster consecutive runs, many users ask for more than one database at setup time.  I will typically be able to provide you with up to six (6) such databases.  Please specify this in your request.

When your work with OrthoMCL is complete, please notify me so that I can purge your databases from the system.

Modifying the Configuration File

Most users will not need to modify the configuration file provided.  The most common modification needed will be to change the name of the database to be accessed in those cases where users are provided with access to more than one database.

The relevant line to be modified is shown below:

 

dbConnectString=dbi:mysql:someUserdb:viking.plantbiology.msu.edu:3306

 

In the example above, the database name is "someUserdb".  

Let's assume (for example), a user had been issued 4 databases named: someUserdb, someUserdb2, someUserdb3, someUserdb4.  To perform a run using one of these other databases, we would need to make a copy of the configuration file and change the name in that file, for example:

 

dbConnectString=dbi:mysql:someUserdb2:viking.plantbiology.msu.edu:3306

 

You may then structure the command for each OrthoMCL run to use the configuration file (and related database) desired.

Backups

A dump of all databases on viking is preformed nightly. As many of these will be retained as space permits, but purges will occur when necessary.  Please contact John Johnston with questions or if you need to find an archived set.

More Information

Refer to the OrthoMCL User Manual.