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PacificBiosciences / pb-human-wgs-workflow-snakemake

Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
BSD 3-Clause Clear License
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lockfile: command not found #134

Closed lauragails closed 1 year ago

lauragails commented 1 year ago

RE line 12 in process sample local:

lockfile -r 0 ${LOCKFILE} || exit 1

I am sure that my environment is loading correctly, and I can see that ./lib/python3.6/site-packages/lockfile was installed in the appropriate place in my environment.

This is how I created the environment I'm using: mamba create -c conda-forge -c bioconda -n pb-human-wgs-debug2 snakemake=6.15.5 lockfile=0.12.2 pysam=0.16.0.1 python=3

However, this line is failing with the error: line 12: lockfile: command not found

A sample command that I used to run step 2 is: ./workflow/process_sample.local.sh sample_ID

How can I find the command and/or make the python software work in the bash context (if this is the right package)?

Thank you!

williamrowell commented 1 year ago

Yeah, lockfile isn't working as expected here. I'll look into it more after Thanksgiving, but the good news is that in the meantime, you can comment line 12 out (and the similar line in process_cohort.local.sh). This is meant to prevent the user from running the same command twice on the same sample at the same time. If you're careful in the meantime, it shouldn't be a problem.

lauragails commented 1 year ago

Got it - yeah I submit with loops so that's not an issue. Will do!

(Happy Thanksgiving)