Define path_to_fauna in config #86
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The current value expects fauna to be a sister directory to 'ingest'. This is valid when we are using the docker runtime¹ as it mounts the 'ingest' folder to '/nextstrain/build' and fauna is 'nextstrain/fauna', but it almost never true when running outside of docker as that would require fauna to be within the 'avian-flu' repo. The docs do state that we must run in docker, but that's an overly strict requirement. Addition context on slack <https://bedfordlab.slack.com/archives/CD84ELG0N/p1723666776588239?thread_ts=1720569955.202459&cid=CD84ELG0N> ¹ until we add a nextstrain-pathogen.yaml file
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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Alternatively, why not add a |
That was done via #87 which sits on top of this PR |
add nextstrain-pathogen.yaml
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The current value expects fauna to be a sister directory to 'ingest'. This is valid when we are using the docker runtime¹ as it mounts the 'ingest' folder to '/nextstrain/build' and fauna is 'nextstrain/fauna', but it almost never true when running outside of docker as that would require fauna to be within the 'avian-flu' repo. The docs do state that we must run in docker, but that's an overly strict requirement.
Addition context on slack https://bedfordlab.slack.com/archives/CD84ELG0N/p1723666776588239?thread_ts=1720569955.202459&cid=CD84ELG0N
¹ until we add a nextstrain-pathogen.yaml file