error when running with profile test about chipseq HOT 5 CLOSED

Hi @rrdavis77 . If you just use -profile test the pipeline will assume that you have all of the software installed locally and available on your PATH. Im assuming this isnt the case. Ideally, you will need to be able to use Docker or Singularity where ever you are running the pipeline. If and when you have this setup you can run the pipeline test using:
nextflow run nf-core/chipseq -profile test,docker or
nextflow run nf-core/chipseq -profile test,singularity

The error itself is coming from the fact that the check_design.py script has been executed with Python 3 which Im assuming is installed locally. However, the pipeline requires Python 2 which is the version installed in the Docker container.

Let me know how you get on.

from chipseq.

You will only need to run the command above to run the tests. Providing you have an internet connection where you are running the pipeline, everything will be downloaded for you.

from chipseq.

Thank you @drpatelh ! I didn't think I could have two options under the flag profile. It is running fine now!
Maybe the installation guide can elaborate and add the fact that you can add the docker or singularity option when running a test. Thank you once again!

from chipseq.

No probs. Yep, a quick start section like the one below will be rolled out in the next release 👍
https://github.com/nf-core/mnaseseq#quick-start

from chipseq.

If you have any further issues or comments please feel free to also ping me on the chipseq channel on the nf-core workspace.

from chipseq.