how can i run looper run without creating env variable '$REFGENIE'

[yqlan]

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]

Hello,

Did you remove the $REFGENIE from the var_templates section of the sample_pipeline_interface?

pepatac/sample_pipeline_interface.yaml

Lines 52 to 53 in ffa7cc2

	var_templates:
	refgenie_config: "$REFGENIE"

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]

Hello @yqlan, did you have success with this?