OrthoMCL

ISU HPC has created a singularity container based on the Docker container from https://hub.docker.com/r/granek/orthomcl/.

These instructions assume that you are working in the same directory as when you downloaded and started the MySQL server container.

1. Get the image:

$ singularity pull --name orthomcl.simg shub://ISU-HPC/orthomcl

2. Prepare the appropriate configuration files . A sample configuration file may be found on the ISU HPC GitHub site.

$ curl https://raw.githubusercontent.com/ISU-HPC/orthomcl/master/orthomcl.config > \ 
    ${PWD}/orthomcl.config

3. Within the MySQL server container, create the orthomcl database.

$ singularity exec instance://mysql mysqladmin create orthomcl

Connecting to the local MySQL server (both containers on same host)

4. Start a shell inside the orthomcl container. Note that we are bind-mounting ${PWD}/mysql/run/mysqld into the container so that the mysql client within the container can communicate with the server running in our first container.

$ singularity shell --bind $PWD \
    --bind ${PWD}/mysql/run/mysqld:/run/mysqld \
    ./orthomcl.simg

5. Within the OrthoMCL container, initialize the orthomcl database.

$ singularity orthomcl.simg:~> orthomclInstallSchema orthomcl.config

6. Run other OrthoMCL commands within the container in a similar fashion.

Connecting to a remote MySQL server (containers on different hosts)

4. Update orthomcl.config to specify a remote database configuration.

dbConnectString=dbi:mysql:orthomcl:localhost
dbLogin=root
dbPassword=my-secret-pw

becomes

dbConnectString=dbi:mysql:orthomcl:HOSTNAME
dbLogin=remote_usr
dbPassword=PASSWORD_FOR_remote_usr

5. Start a shell inside the orthomcl container. Note that we are not bind-mounting ${PWD}/mysql/run/mysqld into the container. Even if ${PWD} is on a network-based file system and shared between the hosts, the local socket is not accessible on the other hosts.

$ singularity shell --bind $PWD ./orthomcl.simg

6. Within the OrthoMCL container, initialize the orthomcl database.

$ singularity orthomcl.simg:~> orthomclInstallSchema orthomcl.config

7. Run other OrthoMCL commands within the container in a similar fashion.