Quick Start

Follow these steps to get started with GenPipes.

Note

New Try GenPipes Wizard

If you are new to GenPipes, we recommend trying the GenPipes Wizard tool. It offers step by step instructions on how to select an appropriate deployment type, select a pipeline, construct the pipeline command and run genomic analysis.

• Step 1: Identify prerequisites

  Review the GenPipes Checklist before you run GenPipes. Make sure you have the required software, hardware, log-in accounts, and other resources required to run GenPipes.

• Step 2: Understand GenPipes basics

  Learn GenPipes basics, concepts, and functionality to apply it to your genomic analysis. Refer to the Introduction to GenPipes and Why GenPipes sections for details.

• Step 3: Select GenPipes deployment

  Explore GenPipes deployment options and select an appropriate one applicable to your use case.

  • GenPipes deployed on the Digital Research Alliance of Canada, DRAC servers, formerly Compute Canada, CCDB servers (This option requires log in and server access. No local software download or deployment required.)

  • GenPipes installed locally on a server, virtual machine, or container *

  • GenPipes deployed in the cloud *

  GenPipes Package for Local Deployment

  Options marked * require you to use one of these options for local deployment:

  • Download the pre-built, packaged GenPipes via the GenPipes Download Page

  • Get the GenPipes Source Code, use the GenPipes Developer Guide and build, deploy it locally.

• Step 4: Review pipeline options

  Check out the available pipelines, use the Pipeline Reference and select an appropriate protocol for genomic analysis. Try the GenPipes Wizard tool to select a GenPipes deployment type, pipeline, and protocol, and construct the full GenPipes command to run the analysis.

• Step 5: Run GenPipes

  Once you have the pipeline command ready with required protocol options, run GenPipes and analyze the results. Check out the GenPipes Tutorials for details.

Usage Change Effective v5.x onward

Using v4.x?

You are recommended to:

• Review the changes in v5.x and v6.x (See tabs)

• Migrate to using the latest GenPipes v6.x

What has Changed?

v6.x

Following changes are effective from GenPipes release v6.x onward:

• Requires Python v3.12.0 or higher.

• A new environment variable ‘GENPIPES_INIS’ is introduced for streamlining access to the config files in the genpipes commands. In the future, ‘MUGQIC_PIPELINES_HOME’ will be deprecated. This is applicable when using GenPipes deployed on the DRAC servers such as Rorqual.

  • Before

    $MUGQIC_PIPELINES_HOME/pipelines/<pipeline>/<pipeline>.base.ini
    

  • Now

    $GENPIPES_INIS/<pipeline>/<pipeline>.base.ini
    

  Note

  Please note that the old variable, ‘MUGQIC_PIPELINES_HOME’ will still be accessible and is still in use for instructions on how to deploy GenPipes locally, in the cloud, or in a container.

• A new Long Read DNA Sequencing pipeline is now available in v6.0 that supports three protocols:

  • Nanopore

  • Nanopore Paired Somatic

  • Revio

v5.x

Following changes are effective from GenPipes release v5.x onward:

• Starting with v5.0, GenPipes uses Python packaging and no longer relies on Python modules.

• If you were using Python v2.7, you must upgrade to Python v3.11.1.

• To run any GenPipes pipelines, use the new command syntax:

  • Old Format

    user@rorqual% <pipeline name>.py [options] -g genpipes_cmd.sh
    user@rorqual% bash genpipes_cmd.sh

  • New Format

    user@rorqual% genpipes <pipeline name> [options] -g genpipes_cmd.sh
    user@rorqual% bash genpipes_cmd.sh

• RNA Sequencing (De Novo) pipeline has been updated in v5.0 release.

• EpiQC pipeline, HiC-Seq pipeline, and AmpliconSeq qiime protocol have been deprecated starting v5.0 onward.

• The DNA-Seq high coverage pipeline and the TumorPair pipeline have been merged into a single workflow DNA-Seq.

• The Methylseq pipeline has a new protocol option using the gemBS aligner in addition to Bismark.

• Genome build GRCh38 (human) is now the default reference genome for all pipelines, but other versions or species can be selected via config files, as before.

  Danger

  When using the mouse genome, please note that the annotation files for GRCm38 do not work with the Homer analysis. Use mm10, instead of the GRCm38 program.

• Markdown style reports have been deprecated for all pipelines starting v5.0 onward and replaced entirely with MultiQC reports.