problem rerun using looper and Error in opt_get_verb() -- solved

[miximimi]

I just start trying PEPATAC and there are two major bugs/issues I encountered, and I am surprised that no one is asking about this on github. I am typing this out just in case someone is facing the same problem.

1. My first looper attempt failed, and when I tried again using looper rerun it fails
   my solution: you need to add one line in sample_pipeline_interface.yaml. This yaml file stores parameter used to run the main python script pipelines/pepatac.py, and for rerun to work, it must take -R or --recover. So you can add a new line -R (or --recover, whichever you prefer) in the chunk for command_template. I added that line after --genome { sample.genome }

2. When running looper an error appears: Error in opt_get_verb() : could not find function "opt_get_verb"
   my solution: modify the R script PEPATAC.R, the line required_libraries <- c("PEPATACr") must be changed to required_libraries <- c("PEPATACr", "optigrab")

I am not sure if I am at the right place to send this post, but I simply hope someone can benefit from this.

[nsheff]

Thank you for posting this @miximimi -- this is the right place.

The first looks like a documentation issue, the second a bug

@donaldcampbelljr can you look into and address these issues?

[donaldcampbelljr]

For item 1, this change was added to PEPATAC for the newest release (v0.11.0).

For item 2, I've added some documentation to the FAQ section.

[miximimi]

Thank you for adding it to the FAQ! Just want to add that when doing looper runp project_config.yaml this same issue happens, and same solution applies: add the -R to project_pipeline_interface.yaml