add nextstrain-pathogen.yaml #87
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This results in a different mount point for the 'ingest' directory in
docker runtimes which more closely matches a typical setup using other
runtimes. This allows the relative location of fauna ('path_to_fauna')
to be the same for a typical ambient setup as for docker.
See <nextstrain/cli#371 (comment)>
for more detail on mount points for the docker runtime.
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are there any additional side-effects of nextstrain-pathogen.yaml I'm not aware of?
I don't think so. The latest version of the pathogen-repo-ci checks for the presence of this file, but this repo's workflow is still pinned to v0.
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Do the ingest or phylogenetic workflows reference other paths outside of themselves? If so, those will change too. |
This'd only be applicable to 'ingest' (phylo is run from the repo level, not a sub directory). In the prior setup, the 'ingest' dir was mounted directly into the container, so there could not be any paths referring to other data within 'avian-flu'. Fauna is the only reference to a path beyond 'ingest', and this was broken for all non-docker runtimes so I'm happy to fix that long-standing bug here. Test ingest action successfully completed now that our rethink server is back up. |
This results in a different mount point for the 'ingest' directory in docker runtimes which more closely matches a typical setup using other runtimes. This allows the relative location of fauna ('path_to_fauna') to be the same for a typical ambient setup as for docker.
See nextstrain/cli#371 (comment) for more detail on mount points for the docker runtime.
@joverlee521 / @tsibley are there any additional side-effects of
nextstrain-pathogen.yamlI'm not aware of?