About OrthoMCL

OrthoMCL is a software used for assigning proteomes to ortholog groups.

About this tutorial

These are the steps I followed to install OrthoMCL on an Ubuntu 14.04 Linux server using MySQL as the database system.

Requirements

1. Ubuntu 14.04 (tested). Might work on other versions.
2. All these steps are done with an user account with admin privileges (sudo).

3. Install MySQL database server (This is an OrthoMCL requirement):

     sudo apt install mysql-server
     sudo service mysql start
   

   The install step will prompt for a password for the MySQL administrator.

4. Install wget and checkinstall. We will use checkinstall to build a debian package (.deb) of OrthoMCL that can be installed, updated or removed easily:

    sudo apt install wget checkinstall
   

Procedure - Install OrthoMCL

Download and uncompress the OrthoMCL archive

wget http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz
tar zxvf orthomclSoftware-v2.0.9.tar.gz

Create a Makefile

To create a debian package using checkinstall, an install step is required (ex: make install). The make command requires a Makefile. As OrthoMCL is a PERL package, we can generate a Makefile by first creating a Makefile.PL.

Change directory:

cd orthomclSoftware-v2.0.9

Using a text editor (ex: nano), create a new file with the following content and save it as Makefile.PL:

use ExtUtils::MakeMaker;

WriteMakefile(
NAME       => 'OrthoMCLEngine::Main::Base',
VERSION    => '2.0.9',
PM         => {'lib/perl/OrthoMCLEngine/Main/Base.pm' => '$(INST_LIB)/OrthoMCLEngine/Main/Base.pm'},
EXE_FILES => ['bin/orthomclAdjustFasta',
'bin/orthomclBlastParser',
'bin/orthomclDropSchema',
'bin/orthomclDumpPairsFiles',
'bin/orthomclExtractProteinIdsFromGroupsFile',
'bin/orthomclExtractProteinPairsFromGroupsFile',
'bin/orthomclFilterFasta',
'bin/orthomclInstallSchema',
'bin/orthomclInstallSchema.sql',
'bin/orthomclLoadBlast',
'bin/orthomclLoadBlast.sql',
'bin/orthomclMclToGroups',
'bin/orthomclPairs',
'bin/orthomclReduceFasta',
'bin/orthomclReduceGroups',
'bin/orthomclRemoveIdenticalGroups',
'bin/orthomclSingletons',
'bin/orthomclSortGroupMembersByScore',
'bin/orthomclSortGroupsFile']
);

Create a Debian package using checkinstall

1. Use PERL to generate a Makefile

    perl Makefile.PL
   

2. Use the generated Makefile to compile source code:

    make
   

3. Create a text file called description-pak with a description for the package like the following:

    An algorithm for grouping proteins into ortholog groups based on their sequence similarity
   

4. Create a directory called doc-pak and copy included documentation.

    mkdir doc-pak
    cp -r doc/OrthoMCLEngine/Main/* doc-pak
   

5. Run checkinstall to create debian package (note: change email address under maintainer)

    sudo checkinstall --install=no --pkgname orthomcl \
    --pkgversion 2.0.9 --pkgrelease 1 --pkglicense gpl \
    --maintainer "you@email.com" --provides orthomcl \
    --exclude /usr/local/lib/perl/5.18.2/perllocal.pod make install
   

   Press ENTER to build the package.

Install generated package

sudo dpkg -i orthomcl_2.0.9-1_amd64.deb

Create a database, configuration file and install schema

1. Create the database, the database user and grant this user permissions to use/update the database.

    mysql -u root -p
   
    create database `orthomcl` character set = 'utf8';
   
    create user 'orthomcl'@'localhost' identified by 'your-password-here';
   
    grant SELECT, INSERT, UPDATE, DELETE, CREATE VIEW, CREATE, INDEX, DROP on `orthomcl`.* to `orthomcl`@localhost;
   
    quit
   

2. For the orthoMclLoadBlast command to work, the local-infile option has to be enabled. Without this option, the command fails with an error - used command is not allowed with this MySQL version. To prevent this, create /etc/mysql/conf.d/client.cnf with the following content (creating this file requires sudo/root privileges):

    [client]
    loose-local-infile=1
   

   Restart MySQL server for the change to take effect:

    sudo service mysql restart
   

3. Most OrthoMCL commands require a configuration file. We can copy the configuration template that is distributed with the software, make changes according to our configuration (i.e., database name, user, password) and then provide that configuration file to the commands.

   Copy template:

    sudo cp /usr/share/doc/orthomcl/orthomcl.config.template /etc/orthomcl.config
   

   Edit this file using a text editor and update configuration:

     dbConnectString=dbi:mysql:orthomcl:mysql_local_infile=1
     dbLogin=orthomcl
     dbPassword=your-password-here
   

4. Install schema:

    sudo orthomclInstallSchema /etc/orthomcl.config install_schema.log
   

   This command should complete without any errors.

(Optional) Create an orthomcl group

This step is optional and is not in the official documentation. When multiple users require access to the database, they can be added to an user group. Only members in this group will have read access to /etc/orthomcl.config. Here is an example:

sudo groupadd orthomcl
sudo gpasswd -a vimal orthomcl

Now update permissions on the file /etc/orthomcl.config:

sudo chgrp orthomcl /etc/orthomcl.config
sudo chmod 640 /etc/orthomcl.config

References

The OrthoMCL user guide.