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Do no create conda environments within cluster jobs by default #1463
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Indeed, that is not intended, all conda envs should be created in the main process before any cluster job is submitted. |
I will have a look. |
williamrowell
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current bug in snakemake 7 causes conda environments to build simultaneously within cluster jobs snakemake/snakemake#1463
johanneskoester
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…file system (fixes issue #1463)
Fixed with PR #1472 |
I had the same problem and can confirm that PR #1472 fixes this for me. |
Thank you very much! |
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Snakemake version
7.1.0
Describe the bug
It seems that in cluster mode, only those conda environments required for local jobs are created locally. The others are created in the cluster jobs. But if there is more than one cluster job with the same conda environment, the jobs try to create the environment at the same time and fail. This happens on a shared distributed file system.
Logs
This is an example log of a cluster job that creates an environment simultaneously with other jobs:
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