Open stianlagstad opened 1 week ago
Excluding tests, there are about 15 hardcoded references to /bin/bash
, most of them related to launching the .command.run
script on a particular executor
I believe the launcher script has certain assumptions baked in around bash
, so it would make sense to point to a different version of bash but not necessarily a different shell
It could make sense as an environment variable or a config option such as executor.bash
I would like to make
/bin/bash
configurable, either through setting an environment variable or through setting a configuration value. Would a PR for this be welcome? Is there anyone I should discuss this with first? Or are there things I should know before I start?One complicating factor I'm aware of is that there may be a need to use one shell on the host system (or the external worker, such as a GCP batch instance), and a different shell inside of the docker/singularity container. Maybe there would be need of two environment variables.
Prior work and comments on this:
/usr/bin/env bash
instead ofbin/bash
, but was rejected. Note the comment from Paolo: "The only solution that I can see is to make the shell path configurable via config setting (env var or config file) which defaults to /bin/bash and the user can change as needed."/bin/bash
to/usr/bin/env bash
. This was not accepted, and closed, due to the previous discussion in the above link.My main motivations for this idea are:
/bin/bash
is not available, and where users can't easily setup a symlink or similar.bash
is used.find . -name "*.groovy" -type f -exec grep -o "/bin/bash" {} + | wc -l
on the current master branch gives 106 results. If there were (many) fewer of these, then other packaging tools would be able to package nextflow and write a small patch which changes the occurrences of these strings.Any input is appreciated. Thank you!