Add readOnlyInputs option for CharliecloudBuilder

[l-modolo]

This merge request is to add the readOnlyInputs option as discussed in the Charliecloud and shared cacheDir #3367 issue.

With this modification:

• the default readOnlyInputs value is false
• if readOnlyInputs is true;
• the -w option is removed from the command
• the bound volumes are transformed to only mount the first folder of the path

For example, if I try to bind /home/user/workdir/ to /home/ the bound path will be /home to /home. By doing that, charliecloud doesn't try to mkdir -p /home/user/workdir/ within the read-only container, the external path is bound at the /home directory level so all the subfolders are accessible with the user rights. If one tries to bind / I added an expection.

ps: Sorry for the code style, it's my first time coding in groovy

Signed-off-by: Laurent Modolo laurent.modolo@ens-lyon.fr

[pditommaso]

Closing since it looks abandoned

[l-modolo]

Hello @pditommaso , we are actively using this patch in my institute since December and it's working as expected. Please tell me if there is anything that I can do.

[pditommaso]

Fair enough, then it may worth to add some unit testing and merge it

[l-modolo]

I added two small checks in the modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy. However I am far from experienced with github CI and I don't know how to run the tests on my fork.

[pditommaso]

Tests run have been approved. However, it's much simpler to test locally just by running the following command in the project root

make smoke module=nextflow

Also, consider signing your commit, see here for details.

[l-modolo]

Hum sorry, the rebase look quite messy, would you prefer to have me make a new merge request from a clean repo ?

[l-modolo]

Dear @pditommaso I cleaned up my master branch to have all my commit signed and the tests that I wrote pass the make smoke module=nextflow command.

[pditommaso]

Nice, All checks have passed! let's merge it. Thanks for this contribution!

[pditommaso]

Sorry @l-modolo, I needed to rever this.

[l-modolo]

No problem, thank you for your great work !

[l-modolo]

Hi @pditommaso I tried to fix the test problem with the last commits of the master branch. It shows 100% of the tests passed for CharlieCloudBuilderTest but LocalRepositoryProviderTest still failed with the following error:

org.eclipse.jgit.api.errors.ServiceUnavailableException: Signing service is not available
	at app//org.eclipse.jgit.api.TagCommand.processOptions(TagCommand.java:247)
	at app//org.eclipse.jgit.api.TagCommand.call(TagCommand.java:115)
	at app//org.eclipse.jgit.api.TagCommand.call(TagCommand.java:1)
	at nextflow.scm.LocalRepositoryProviderTest.should list tags(LocalRepositoryProviderTest.groovy:132)

[pditommaso]

What if you run make smoke ?

[l-modolo]

It give me the same error for :

LocalRepositoryProviderTest
should list tags | 0.019s | failed

However, the CI for github seems fine https://github.com/l-modolo/nextflow/actions/runs/4052972167

[pditommaso]

Try creating a new PR. I'll double check in my env

[l-modolo]

Hi @pditommaso I created the #3590 PR

[pditommaso]

Thanks a lot, in the pipeline