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kusterlab / prosit

Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7
https://www.proteomicsdb.org/prosit/
Apache License 2.0
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Installing Prosit #45

Closed MiguelCos closed 4 years ago

MiguelCos commented 4 years ago

Hello,

We have been very happy with our tests using Prosit on the proteomicsDB website but we would like to be able to scale-up our analysis capabilities by using Prosit locally.

We set up a Windows server (Windows Server 2019) with an NVIDIA Quadro P400 GPU (CUDA enabled) and I am trying to set up Prosit on it but it is proving to be of some challenge to me so far. I have little experience with Docker and containers so I would really appreciate any guidance you can offer.

So far, I have installed the Native Windows Docker client, which seems to work nicely on Windows Server 2019 and I am currently in the process of installing nvidia-docker. I am not sure if I understand this correctly, but I believe I would be possible to install nvidia-docker with the Windows Docker client. Am I correct?

From the nvidia-docker wiki: grafik

I hope this is not terribly silly, but by looking the dockerd documentation I am still completely lost on the next steps I should follow to install nvidia-docker.

It seems that it would be simpler if I would be able to install Windows Subsystem for Linux 2 (WSL 2) and then install docker and all the dependencies throgh the linux subsystem, but it seems that WSL 2 (the distro version allowing docker installations) is still not part of the standard Windows Server 2019 build and it would be required to install a windows insiders preview version.

I would really appreciate any guidance.

All the best, Miguel

LLautenbacher commented 4 years ago

Hi Miguel,

since all our Prosit instances are running and were developed on Linux. I'm afraid that I can't help you. And also don't know anybody that I could refer you to.

If you find a way to use Prosit on a Windows server it would be awesome if you let us know!

Best, Ludwig