Ability to jump out of cycling stage early

[aaronmck]

Just curious if there's any documentation on the deployment process -- we have a Chai RT machine and I'd love to add a couple basic features for skipping out of stages in real time.

[jperfetto]

We don't have much dev documentation yet, but to deploy we basically run "gulp deploy" in the chaipcr directory, and then use the deploy.sh script passing the IP of your machine as an argument (like ./deploy.sh 10.0.x.x).

May you explain more about why you want to skip out of stages in real time?

[aaronmck]

Thanks, that sounds like a place to start!

There are a couple of reasons to skip out of a stage. Say you're amplifying up a sequencing library, where over amplification can skew your library towards things that amplify more easily (GC bias, etc). In cases like this you want to watch the curves come up, so you have enough material, but stop amplifying before the curves saturate.

I'm happy to take a go at putting this into the real time code and plumbing it up the main screen,
or hand it off to someone.

[jperfetto]

And why do you want to skip out, as opposed to simply aborting the protocol early?

[aaronmck]

We'd like to skip out instead of aborting so that any final extension step can be run (the next stage), and the library can be cooled to 4C (the final stage), stopping any additional activity.

[jperfetto]

I see. We're thinking to implement a way to modify the number of cycles while an experiment is in progress. I think this will accommodate your use case, as well as people who wish after the fact they had specified more cycles. Will that work?

[aaronmck]

Great, I think that would be a much more flexible solution.

[jperfetto]

Ok, we will be adding this feature, it will probably take around 6 weeks. I'll re-purpose this issue for it.