line 3: docker: command not found

[ccrobertson]

Hi Nathan,

I am working on updating my PEPATAC installation on Rivanna (last time I installed it was in Nov 2019). I see it now uses bulker to handle containers. I have installed bulker and loaded the pepatac container using the following from the pepatac documentation:

bulker load databio/pepatac:1.0.4 -r bulker activate databio/pepatac:1.0.4

however, when i then try to run commands (e.g. the pepatac example, or even "cat filename" to look at a file), i get the error

/home/ccr5ju/bulker_crates/databio/pepatac/1.0.4/cat: line 3: docker: command not found

I'm guessing this has to do with the fact that Rivanna does not support docker. Is there an option I need to provide to indicate that singularity must be used instead?

Thanks for the help!

[ccrobertson]

UPDATE:

This error message also happens with the bulker demo example:

bulker activate demo Using default config. No config found in env var: BULKERCFG Bulker config: /home/ccr5ju/.local/lib/python3.6/site-packages/bulker/templates/bulker_config.yaml Activating bulker crate: demo /home/ccr5ju/.local/lib/python3.6/site-packages/bulker/bulker.py:762: UserWarning: The '_file_path' property is deprecated and will be removed in a future release. Use YacAttMap["__internal"][_file_path] instead. os.path.dirname(bulker_config._file_path)) [\033[01;93m]bulker/demo|[\033[00m][\033[01;34m]\w[\033[00m]\$

bulker/demo|~/software$ cowsay "hello" /home/ccr5ju/bulker_crates/bulker/demo/default/cowsay: line 3: docker: command not found

[nsheff]

Hi, did you run a bulker init at all? it should automatically detect that you have only singularity installed and work, but you'd need to initialize.

If you didn't bulker init to create your own config, then bulker may be using the default config, which defaults to docker.

[ccrobertson]

UPDATE 2:

I used the autogeneration of the config file using bulker init -c $BULKERCFG as described here: https://bulker.databio.org/en/latest/install/

This works now! Before I had manually edited the container engine field in the provided config file, but not very carefully.

Sorry for the trouble!

[nsheff]

wow, great! glad it worked. you might need to tweak some other configuration options in the bulker config to get it to work, to make sure the containers have access to all the necessary information.