Accessing GenPipes on Compute Canada Servers

This document will provide information on how to get started with using GenPipes pre-installed on Compute Canada servers.

Step 1: Get a Compute Canada Data Base (CCDB) account

  1. Go to the website: https://ccdb.computecanada.ca/account_application

  2. Agree with the policy and submit your acceptance

  3. Fill the form and submit it.

Note

If you are a student or a post-doc (or any other kind of Sponsored User), to be eligible to apply to Compute Canada, the Principle Investigator (PI) of your laboratory must also have an account. You will need the Compute Canada Role Identifier (CCRI) of your sponsor/PI. The CCRI has the abc-123-01 form. It is free for Canadian academics to use the Compute Canada servers.

It will take one or two days before your account request is processed.

Step 2: Connect to Compute Canada servers

Unix / Linux / Mac or Windows (bash)

  1. Open a shell or terminal (bash preferably) and type the following command:

ssh myaccount@mp2b.ccs.usherbrooke.ca

  1. Enter your Compute Canada account password.

Windows (PuTTY)

  1. Open puTTY.

  2. Select “Session” on the left hand side panel

  3. Select “SSH” and fill the “Host Name” entry with the following:

mp2b.ccs.usherbrooke.ca

  1. Click “Open”

A terminal will open and ask you to connect using your CC account credentials.

Voila!!! You are all set to use GenPipes deployed on Compute Canada data centre.

Note

Canadian Centre for Computational Genomics (C3G), in partnership with Compute Canada, offers and maintains a large set of bioinformatics resources for the community. For a complete list of software currently deployed on several HPC centres, including Guillimin, Cedar, Graham and Mammouth, refer to Bioinformatics Resources. Several reference genomes are also available. You can refer to the available genomes and the environment setup to access these genomes.

Step 3: Setting up your user environment for GenPipes access

For Abacus, Compute Canada Users only

All of the software and scripts used by GenPipes are already installed on several Compute Canada servers including Guillimin, Mammouth, Cedar and Graham, and will soon be installed on Beluga. To access the tools, you will need to add the tool path to your bash_profile. The bash profile is a hidden file in your home directory that sets up your environment every time you log in. You can also use your bashrc file.

Genomes and modules used by the pipelines are already installed on a CVMFS partition mounted on all those clusters in /cvmfs/soft.mugqic/CentOS6

Note

For more information on the differences between the .bash_profile and the .bashrc profile, consult this page.

## open bash_profile
nano $HOME/.bash_profile

Note

GenPipes have been tested with Python 2.7

Next, you need to load the software modules in your shell environment that are required to run GenPipes. For a full list of modules available on Compute Canada servers see the module page

To load the GenPipes modules, paste the following lines of code and save the file, then exit (Ctrl-X):

umask 0002

## GenPipes/MUGQIC genomes and modules
export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
module use $MUGQIC_INSTALL_HOME/modulefiles
module load mugqic/python/2.7.14
module load mugqic/genpipes/<latest_version>
export JOB_MAIL=<my.name@my.email.ca>
export RAP_ID=<my-rap-id>

You will need to replace the text in “<>” with your account and GenPipes software version specific information.

JOB_MAIL is the environment variable that needs to be set to the email ID on which GenPipes job status notifications are sent corresponding to each job initiated by your account. It is advised that you create a separate email for jobs since you can receive hundreds of emails per pipeline. You can also de-activate the email sending option by removing the “-M $JOB_MAIL” option from the .ini files.

RAP_ID is the Resource Allocation Project ID from Compute Canada. It is usually in the format: rrg-lab-xy OR def-lab.

Environment settings for MUGQIC analysts

For MUGQIC analysts, add the following lines to your $HOME/.bash_profile:

umask 0002

## MUGQIC genomes and modules for MUGQIC analysts

HOST=`hostname`;

DNSDOMAIN=`dnsdomainname`;

export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6

if [[ $HOST == abacus* || $DNSDOMAIN == ferrier.genome.mcgill.ca ]]; then

  export MUGQIC_INSTALL_HOME_DEV=/lb/project/mugqic/analyste_dev

elif [[ $HOST == ip* || $DNSDOMAIN == m  ]]; then

  export MUGQIC_INSTALL_HOME_DEV=/project/6007512/C3G/analyste_dev

elif [[ $HOST == cedar* || $DNSDOMAIN == cedar.computecanada.ca ]]; then

  export MUGQIC_INSTALL_HOME_DEV=/project/6007512/C3G/analyste_dev


elif [[ $HOST == beluga* || $DNSDOMAIN == beluga.computecanada.ca ]]; then

  export MUGQIC_INSTALL_HOME_DEV=/project/6007512/C3G/analyste_dev

fi

module use $MUGQIC_INSTALL_HOME/modulefiles $MUGQIC_INSTALL_HOME_DEV/modulefiles
module load mugqic/python/2.7.14
module load mugqic/genpipes/<latest_version>

export RAP_ID=<my-rap-id>

Also, set JOB_MAIL in your $HOME/.bash_profile to receive PBS job logs:

export JOB_MAIL=<my.name@my.email.ca>

How to check the version of GenPipes deployed

To find out the latest GenPipes version available, once you have connected to your CC account, use the following command:

module avail 2>&1 | grep mugqic/genpipes

Note

Previous version of GenPipes were named mugqic_pipelines and are still available for use.

How to ensure bash_profile changes take effect in the environment variables?

When you make changes to your bash_profile, you will need to log out and then login again for these changes to take effect. Alternatively, you can run the following command in bash shell:

source $HOME/.bash_profile

By adding the lines related to module load and environment variable setting via export, you have set up the pipeline environment and are ready to use GenPipes!

This also gives you access to hundreds of bioinformatics tools pre-installed by our team. To explore the available tools, you can type the following command:

module avail mugqic/

For a full list of all available modules on Compute Canada servers, visit module page.

To load a tool available on Compute Canada servers, for example - samtools, use the following command:

# module add mugqic/<tool><version>
module add mugqic/samtools/1.4.1

# Now samtools 1.4.1 is available for use in your account environment. To check, run the following command:
samtools

Several of the GenPipes pipelines may require referencing genomes. To access these pre-installed genomes available in:

$MUGQIC_INSTALL_HOME/genomes/species/

use the following command to check all available genome species:

ls $MUGQIC_INSTALL_HOME/genomes/species

All genome-related files, including indices for different aligners and annotation files can be found in:

$MUGQIC_INSTALL_HOME/genomes/species/<species_scientific_name>.<assembly>/
## so for Homo Sapiens hg19 assembly, that would be:
ls $MUGQIC_INSTALL_HOME/genomes/species/Homo_sapiens.hg19/

For a complete list of all available reference genomes, visit genome page.

Step 4: Running GenPipes pipelines

Now you are all set to run GenPipes analysis pipelines. Refer to instructions in Using GenPipes for genomic analysis for example runs. For specific pipelines supported by GenPipes, their command options refer to GenPipes User Guide.