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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Docker vs Nextflow #202

Open DrDee79 opened 3 years ago

DrDee79 commented 3 years ago

I am having issues as I can't run Docker on my laptop and our big processing machine is running Windows Server (it's a VM) which won't run Docker without $$$. Is there a way to get into Nextflow or something similar that can run on this option?

trishorts commented 3 years ago

You can actually put docker containers inside of nextflow. We do that here with a MetaMorpheus docker https://github.com/sheynkman-lab/Long-Read-Proteogenomics

I'm don't think that we have the human resources available to do that at the moment. But if you know someone familiar with Nextflow, this should be pretty straightforward.

DrDee79 commented 3 years ago

Thank you this is great! I think several people in our comp sci work with Nextflow which is why I mentioned it.

trishorts commented 3 years ago

I havent' done this myself. But, I think you need to make sure that you provide a directory that the docker can write to for its output when you put this all inside of nextflow. And, I think the docker may be at a directly level below what you imagine it to be. I'm probably talking nonsense, but maybe you can share this with your nextflow people and they will understand what I mean.

acesnik commented 3 years ago

Hi there, you can also run Spritz on the commandline, and I've updated it today, so that it's able to run on protected-access servers without open internet access. That might be an option here.