Multiple users run same pipeline in Snakemake: metadata permissions issue

Programming
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1

We want to store our pipeline in a shared space so that all our analysts have access to it. However, when one person runs the pipeline, the files in the .snakemake/metadata directory belong to that user, and when another user tries to run it, they can’t access the metadata, causing an error.

We would prefer to have users be able to run the pipeline in parallel, but our current setup means this is not possible. All users are within the same group, but this does not help.

Are there any suggestions for solving this issue?

2

One solution is to change the permissions on the .snakemake/metadata directory to allow all users in the group to access it. This can be done using the chmod command. For example, chmod g+rwx .snakemake/metadata would give the group read, write, and execute permissions on the metadata directory. This should allow all users in the group to access the metadata and run the pipeline in parallel.