QIIME Docker image always caching when used with cwltool

[johnbradley]

I am attempting to use the qiime2/core:2018.6 docker image with cwltool.
Every time I run a command it prints out the following message:

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.

This is due to how cwltool creates a temporary home directory for each command run. This helps create a sanitary environment for running commands. Unfortunately this throws away the qiime2 cache.

I was able to work around this by creating my own docker images specifying a value for XDG_CONFIG_HOME:

FROM qiime2/core:2018.6
ENV XDG_CONFIG_HOME /qiime2_cache
RUN qiime dev refresh-cache
CMD bash

Do you know of any issues with using this approach to store the qiime2 cached data inside the docker image?

Thanks.

[thermokarst]

@johnbradley

I was able to work around this by creating my own docker images specifying a value for XDG_CONFIG_HOME

@johnbradley

Do you know of any issues with using this approach to store the qiime2 cached data inside the docker image?

Sounds reasonable to me - we do something similar in the official image: vm-playbooks/docker/Dockerfile at master · qiime2/vm-playbooks · GitHub

I wonder if there is something we could do different in the future to make the official image more portable?

Anyway, thanks for checking, keep us posted!

[johnbradley]

Thanks for the quick response.

I think if you added something like ENV XDG_CONFIG_HOME /qiime2_cache above the RUN qiime dev refresh-cache in your docker file it would fix this for the official image. If you are interested in such a change I could create a PR.

[thermokarst]

Thanks @johnbradley!

@johnbradley

If you are interested in such a change I could create a PR.

A PR would be great! Thanks! :qiime2: