3

I am trying to execute a Snakemake workflow on AWS, and have succeeded in executing my workflow using the command:

snakemake --tibanna --use-conda --default-remote-prefix=mybucket/myproject

and it works successfully. So far, so good. Unfortunately snakemake keeps running in the foreground in the terminal until the workflow ends. Using Ctrl-C on it ends the run. This is problematic for me when I want to run a pipeline that takes a few days.

Is there a way to run pipelines using snakemake --tibanna and detach and poll the results later?

I believe tibanna has the capability: tibanna run_workflow runs the workflow and detatches, and you can check the status later using tibanna stat. I just can't get snakemake to finish leaving the processes scheduled in the cloud.

Muhammad Alkarouri
  • 23,884
  • 19
  • 66
  • 101
  • Have you tried using `nohup` (see https://en.wikipedia.org/wiki/Nohup#Use)? – bli Dec 09 '20 at 08:36
  • 1
    It doesn’t cover what I want. I want to trigger the computation in the cloud and shut down my computer, not keep the process working in the background. – Muhammad Alkarouri Dec 09 '20 at 12:06

0 Answers0