Nathan Sheffield

you can also now use `-p` to not update prompts if you want to just keep using your default prompt.

The bulker config is a YacAttMap, which is a PathExAttMap -- so in theory it should be expanding those env vars... but it doesn't Writing the config uses the `.to_yaml()`...

This all makes sense, and you're right, I think it's the way it should be. So, what I'm looking for is `to_yaml(expand=True)`. Raised an issue there.

I updated the demo to avoid the problem with bulker run for now.

Hmm, is it just a case of needing to not map the user? Are you using `no_user` mode? https://bulker.databio.org/en/latest/advanced_templates/ I don't quite understand the final thing about the rstudio-server one...

This seems like some kind of problem with clang in the `waldronlab/bioconductor:release ` image You *could* just add `no_user` to that image's settings in your bulker config. That solves the...

here are a few related things I found: - https://stackoverflow.com/questions/45122459/docker-mounts-denied-the-paths-are-not-shared-from-os-x-and-are-not-known - https://github.com/localstack/localstack/issues/480 - https://github.com/docker/for-mac/issues/2396 Maybe `/etc` needs to show up in that graphical interface as shared by MacOS? Otherwise, your...

singularity is not correctly pulling that image... can you do this independet of bulker? ``` singularity pull rpipe docker://databio/rpipe ```

If you can't do "singularity pull rpipe docker://databio/rpipe" in general, then there's some problem with singularity that is not related to bulker. might need to ask the sys admins or...

well, bulker puts it in a specific spot that it manages, so you'd be best of now using bulker to build it... you can type: `bulker load -b databio/pepatac`, for...