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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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how can i run `looper run` without creating env variable '$REFGENIE' #251

Open yqlan opened 1 year ago

yqlan commented 1 year ago

I run the following command,

looper run -d --package singularity atacSeq_protocolTest.yaml

without using refgenie, but just using --genome_index and --chrom_sizes

and i got the error: FileNotFoundError: [Errno 2] No such file or directory: '$REFGENIE'

Does that mean I must create the env variable $REFGENIE? how can i just use --genome_index and --chrom_sizes to run the pipeline? I appreciate if anyone can help.

donaldcampbelljr commented 10 months ago

Hello,

Did you remove the $REFGENIE from the var_templates section of the sample_pipeline_interface? https://github.com/databio/pepatac/blob/ffa7cc23ff9b11483f1ab317670d06bb886d6288/sample_pipeline_interface.yaml#L52-L53

var_templates:
  refgenie_config: "$REFGENIE"

You would need to set the path to the refgenie_config, though, as I believe that is the easiest way to use those attributes.

donaldcampbelljr commented 1 month ago

Hello @yqlan, did you have success with this?