Atlas issues

[Astahlke]

Running on atlas brings up a bunch of issues.

• Trying to generate histograms for purge_dups:

Traceback (most recent call last):
  File "/project/ag100pest/software/purge_dups/scripts/hist_plot.py", line 4, in <module>
    import matplotlib as mpl

• For BUSO, you can either kick to the process to queue='service' in configs/atlas.config or direct to an offline directory, eg

    --offline \
   --download_path /project/ag100pest/busco_datasets

[j23414]

Just a note that hist_plot.py is deprecated for our pipeline, but please let me know if I'm mistaken.

Good note on BUSCO, sounds like we can modify busco_params for Atlas.

--busco_params                 Parameters passed to busco [default: ' -l insecta_odb10 -m genome -f ']

Or something like:

nextflow run isugifNF/polishCLR -r main \
   --busco_params " -l insecta_odb10 -m genome -f --offline --download_path /project/ag100pest/busco_datasets" \
   # rest of the arguments . . .

which gets dropped in here:

https://github.com/isugifNF/polishCLR/blob/d1a1b9f8b08132a6f5715f774c0ddb915983bdce/modules/busco.nf#L33-L37