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.
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.
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.