databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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divvy is not using the correct template directory #294

Closed nsheff closed 1 month ago

nsheff commented 1 month ago
divvy list
Using divvy config: /project/shefflab/rivanna_config/divcfg/uva_rivanna.yaml
Available compute packages:

parallel
singularity_local
default
sigterm
bulker_slurm
largemem
local
singularity_slurm
bulker_local

in that config (uva_rivanna.yaml) I see:

  bulker_slurm:
    submission_template: divvy_templates/slurm_bulker_template.sub
    submission_command: sbatch

And that template file exists in the right place:

ll /project/shefflab/rivanna_config/divcfg/divvy_templates/slurm_bulker_template.sub 
-rwxrwx---+ 1 ns5bc shefflab 413 Apr 20  2020 /project/shefflab/rivanna_config/divcfg/divvy_templates/slurm_bulker_templ

Yet, when I try to use it:

looper run -d -l 1 -p bulker_slurm

Looper is trying to get the built-in divvy config!

...ile "/home/ns5bc/.local/lib/python3.11/site-packages/looper/divvy.py", line 344, in write_script
    return write_submit_script(output_path, self.template(), variables)
                                            ^^^^^^^^^^^^^^^
  File "/home/ns5bc/.local/lib/python3.11/site-packages/looper/divvy.py", line 104, in template
    with open(self.compute["submission_template"], "r") as f:
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/ns5bc/.local/lib/python3.11/site-packages/looper/default_config/divvy_templates/slurm_bulker_template.sub'

So, looper appears to be using the wrong divvy config, for some reason.

echo $DIVCFG
/project/shefflab/rivanna_config/divcfg/uva_rivanna.yaml
nsheff commented 1 month ago

Oops, wrong repo. Moved here: https://github.com/pepkit/looper/issues/530