GenPipes Developers

Pytest command on CCDB server results in command not found error. Pytest install fails.

A new developer trying to setup and run GenPipes tests found the following issues:

I am trying to run some python test cases using "pytest" on beluga cluster.
I am running into "pytest command not found " error.
../_images/pytest-err1.png
I googled that error and found that it might be due to older version of setup tools.
I tried to upgrade it and I'm seeing this error now.
../_images/pytest-err2.png

Response

Once your account is activated, you can login in CCDB servers such as Beluga, Cedar, Niagra. However, these are National Systems on a shared grid and users don’t have permission to install or upgrade the software there.

For more information on what software is installed on Compute Canada infrastructure, refer to https://docs.computecanada.ca/wiki/Available_software.

What kind of further analysis be done using HiC sequencing Pipeline?

Response

GenPipes Real Life Applications section of the documentation states that the Hi-C pipeline’s further analyses may integrate ChIP-seq/RNA-seq data. Refer to the Bait Intersect and Capture Intersect steps of the pipeline. These steps help to integrate ChIP-seq / RNA-seq data. You can see which of your regions have ChIP-seq or RNA-seq signal.