Updated deploy script

[Jakob37]

Description and reviewer info

What is changed? How does this update improve the pipeline? (For reviewers) How to test it?

For reviewers. It would be great to:

• Check whether valid
• Check whether it is missing something important
• Do a test run (abort before deploy, or deploy to a different test location)

A new more verbose (and error safe) deploy script. Here is how it communicates with the deployer:

Checks:

• Whether on master branch. If not, prompted on whether to continue
• Reminder to check whether there are running jobs
• Shows compact diff, asks whether you want to inspect the full diff
• Do you want to deploy

jakob@laptop:~$ bash <home>/src/wgs/scripts/deploy_hopper_new.sh 
> Current working directory: <home>/src/wgs
> You are not on the master branch. Current branch: jw/updated_deploy_script
> Do you want to deploy anyway? (y/n)
y
> Confirm, there are no running jobs for this pipeline? (y/n)
y
> Retrieving current git.hash from <fs1>:<basedir>/wgs_germline38/git.hash, please wait ...
> Showing diff to c07a8c0
 scripts/deploy_hopper_new.sh                     | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 scripts/{ => deprecated}/deploy_hopper.sh        |  0
 scripts/{ => deprecated}/deploy_hopper_dev_38.sh |  0
 scripts/{ => deprecated}/deploy_trannel.sh       |  0
 4 files changed, 61 insertions(+)
> Do you want to view the full diff? (y/n)
n
> Do you want to proceed with deploying? (y/n)
n
Deploy aborted

I also moved the deploy scripts which I think are unused to a "deprecated" subfolder. I think we could remove these if we know they won't be used. I left the "dev" script I think @ViktorHy is using.

Type of change

• [x] Documentation (actually utils like this seems like a different category @alkc )
• [ ] Patch
• [ ] Minor change
• [ ] Major change

Checklist

• [x] Self-review of my code
• [x] Update the CHANGELOG
• [ ] Tag the latest commit (vX.Y.Z format)
• [ ] Log samples used for testing in the Verification_samples_log Excel sheet

Documentation

• [ ] At least one other person has reviewed my changes (not required for trivial changes)

Patch

• [ ] Stub run completes without errors or new warnings
• [ ] At least one other person has reviewed and approved my code (not required for trivial changes)

Major / Minor change

• [ ] Stub run completes without errors or new warnings
• [ ] onco run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] wgs single run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] wgs trio run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] At least one other person has reviewed and approved my code
• [ ] I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

• [ ] Alexander
• [ ] Jakob
• [ ] Paul
• [ ] Ryan
• [x] Viktor

(Add if missing)

Testing performed by

• [ ] Alexander
• [x] Jakob
• [ ] Paul
• [ ] Ryan
• [x] Viktor

[ViktorHy]

I guess the dev-deploys really dont need to be a part of the repo. I can just keep those as untracked files in my local folders.

[ViktorHy]

ah good you caught the scp part

[ViktorHy]

Tested it now, works fine!

[Jakob37]

Thanks for the testing!

A small caveat is that if deploying with uncommited changes, the working directory will be deployed, but the git.hash is from the HEAD. Hopefully people will get this anyway, but if not we could add extra checks in the future.