Frequently asked questions

Queries related to GenPipes and its usage are categorized broadly as follows:

• General

• New Users

• GenPipes Developers

• C3G Resources

• GenPipes HPC Jobs

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Contents

• General
  • What is GenPipes?
  • Where can I find GenPipes Citation reference and text?
  • Where can I access latest GenPipes source code?
  • Do I need to deploy GenPipes locally on a server or in the cloud to use it?
  • GenPipes requires familiarity with Unix. As a Windows user, what do I need to setup to use GenPipes?
  • Where do I find tips on troubleshooting GenPipes runtime and usage issues?
  • For new developers, are there any GenPipes development and troubleshooting tips?
• New Users
  • To create a new CCDB account, what should I fill in the form field: ‘position’?
  • What email ID should I use if I am an external collaborator?
  • My account is activated. How do I learn more about Compute Canada Servers and resources available?
  • My account is activated but I cannot login into beluga-computecanada or any other node - Cedar, Niagra? What is wrong?
  • What is the best place to report GenPipes bugs?
  • I was trying to use GenPipes deployed in a Docker Container. What <tag> value should I use?
  • How do I run GenPipes locally in my infrastructure using a containerized setup? Is a scheduler setup necessary?
  • GenPipes 3.4 RNA Sequencing Pipeline moved from using Trimmomatic to Skewer. Why? What does this change mean for GenPipes users?
• GenPipes Developers
  • How do I modify parameters/ options for specific tools or change computational resources that require a job to run?
  • Pytest command on CCDB server results in command not found error. Pytest install fails.
  • What kind of further analysis be done using HiC sequencing Pipeline?
• C3G Resource Usage
  • Where can I find more details on CCDB servers, file system, usage guidelines?
  • Is there a list of software installed on Compute Canada servers?
  • What are modules and why do we need them for GenPipes?
  • What are GenPipes genomes? Where can I access them from?
  • What is meant by test dataset? Where can I find available test datasets?
• GenPipes HPC Jobs
  • How do I run GenPipes pipelines when the number of steps or jobs exceeds HPC site queue limit?
  • In case of an error or job timeout, do I need to re-run the entire GenPipes Pipeline script over again or is there a smarter way to submit only the failed jobs?