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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 $REFGENIE? how can i just use --genome_index and --chrom_sizes to run the pipeline? I appreciate if anyone can help.
The text was updated successfully, but these errors were encountered:
yqlan
changed the title
looper run doesn't work, [Errno 2] No such file or directory: '$REFGENIE'
how can i run looper run without creating env variable '$REFGENIE'
Oct 4, 2023
I run the following command,
looper run -d --package singularity atacSeq_protocolTest.yaml
without using refgenie, but just using --genome_index and --chrom_sizes
and i got the error: FileNotFoundError: [Errno 2] No such file or directory: '$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.
The text was updated successfully, but these errors were encountered: