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Report Augur versions on error without --use-conda #611

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@huddlej huddlej commented Apr 19, 2021

Description of proposed changes

If the workflow errors out and the user isn't using the --use-conda Snakemake flag, let the user know what Augur version they have installed and which version is expected in the Conda environment. Let users know about the --use-conda flag in this case as a possible solution to the workflow errors.

Previously, we've attempted to assert minimum Augur versions in the Snakefile, but this is difficult to assert under all valid conditions (e.g., when the user uses --use-conda, we don't know what Augur version they have). This PR attempts to handle the case when users do not use the workflow's predefined Conda environment and at least a) report their current Augur version and the required version based on the Conda environment file and b) let them know about the --use-conda flag. This approach opts for providing a more helpful error message to users when the workflow fails instead of asserting a requirement that is difficult to verify prior to running the workflow.

Related issue(s)

Related to nextstrain/cli#119

Testing

Tested by installing an older version of Augur in an external Conda environment that did not support the --output-strains argument for augur filter (11.1.2 or before) and confirming that the new error message about --use-conda got printed when the filter rule failed.

Release checklist

If this pull request introduces new features, complete the following steps:

  • Update docs/change_log.md in this pull request to document these changes by the date they were added.

If the workflow errors out and the user isn't using the `--use-conda`
Snakemake flag, let the user know what Augur version they have installed
and which version is expected in the Conda environment. Let users know
about the `--use-conda` flag in this case as a possible solution to the
workflow errors.
@rneher
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rneher commented Apr 7, 2023

@huddlej this might still be useful and has not merge conflicts!!!

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