missing python package
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When I run the test data, it dies with this error:
Error executing rule sankey_diagram on cluster (jobid: 213, external: Submitted batch job 33397859, jobscript: /scratch/sahlab/RC2_IBD_virome/te
st/.snakemake/tmp.1edmh2g2/snakejob.sankey_diagram.213.sh). For error details see the cluster log and the log files of the involved rule(s).
Job failed, going on with independent jobs.
[Thu Oct 28 01:20:39 2021]
Finished job 196.
214 of 216 steps (99%) done
Exiting because a job execution failed. Look above for error message
Complete log: /scratch/sahlab/RC2_IBD_virome/test/.snakemake/log/2021-10-27T220225.813094.snakemake.log
ERROR: Snakemake command failed
ERROR:snakemake.logging:RuleException:
ValueError in line 501 of /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/snakemake/workflow/rules/04_summaries.smk:
Image export using the "kaleido" engine requires the kaleido package,
which can be installed using pip:
$ pip install -U kaleido
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 2357, in run
_wrapper
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/snakemake/workflow/rules/04_summaries.smk", line 501, in __rule_sankey_diagram
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/basedatatypes.py", line 3821, in write_image
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/io/_kaleido.py", line 268, in write_image
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/plotly/io/_kaleido.py", line 134, in to_image
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 574, in _cal
lback
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/concurrent/futures/thread.py", line 52, in run
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 560, in cach
ed_or_run
File "/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb2/lib/python3.9/site-packages/snakemake/executors/init.py", line 2390, in run
_wrapper
Fix is in dev and will be in the next build.