Getting Started:

Abacus, Compute Canada users

Software and scripts used by GenAP_Pipes are already installed on several Compute Canada servers including Guillimin and Mammouth and will soon be installed on Cedar and Graham. 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. For more information on the differences between the .bash_profile and the .bashrc profile, consult this page

## open bash_profile:
nano $HOME/.bash_profile

paste the following lines of code and save the file and Exit (Control + X):

## MUGQIC genomes and modules
export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
module use $MUGQIC_INSTALL_HOME/modulefiles
module load mugqic/python/2.7.13
module load mugqic/GenAP_Pipes/3.0.0
export JOB_MAIL=<my.name@my.email.ca>
export RAP_ID=<my-rap-id>
## for Graham and Cedar users:
export RAC_ID=<my-rac-id>

You will need to replace text within < >, with your information.

To find out the latest GenAp_Pipes version use the output of:

module avail 2>&1 | grep mugqic/GenAP_Pipes

RAP_ID is the Resource Allocation Project ID from Compute Canada. It is usually in the format: abc-123-ab

RAC_ID is the Resource Allocation Project ID from Compute Canada; It is the same thing as the RAP_ID but has been renamed in the newer clusters.

 

When you make changes to your bash_profile, you will need to log out then log in again, or type in the following command:

source $HOME/.bash_profile

By adding those lines to your bash profile, you are now ready to use our pipelines. This also gives you access to hundreds of bioinformatics tools pre-installed by our team. To explore the available tools, you can type:

module avail mugqic/

 

To load a tool, for example samtools, you can use:

# module add mugqic/<tool>/<version>
module add mugqic/samtools/1.4.1
# Now samtools 1.4.1 is available to use. To check:
samtools -h

You also have access to pre-installed genomes available in: $MUGQIC_INSTALL_HOME/genomes/species/
To check all the available species, type:

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/

 

You are now set up to use the pipelines. Check out the sections below to learn how to launch pipelines and to access toy datasets to practice.

Available pipelines
How to Launch a pipeline?
How to create a Readset file?
How to edit Configuration/ini files?
How to create a Design file?
Toy dataset: Hi-C data
Toy dataset: ChIP-Seq data
Toy dataset: RNA-Seq data

 

For more information:

Our pipelines are built around third party tools that the community uses in particular fields. To understand the output of each pipeline, please read the documentation pertaining to the tools that produced the output.

For more information or help with particular pipelines, you can send us an email to:
info@computationalgenomics.ca

Or drop by during our Open Door slots.
We are located at:

740 Dr. Penfield avenue, room 4200
Montréal, QC H3A 1A5