Closed Munchic closed 2 years ago
Hi, for reading .raw files directly, without conversion to .mzML, please use the Windows version of DIA-NN under Windows or Wine.
Best, Vadim
Hi Vadim,
Thank you, I will try to run them through Wine.
Sincerely, Khoi
@vdemichev Is there a way to run DiaNN in Wine through the command line directly without running the setup first (because that would require a GUI input). I am trying to set up an automated cloud job for processing raw files with DiaNN which will run it in Ubuntu-based Docker with Wine. Because it's an automated job, I can't have graphical interface installation there. Let me know if my question makes sense, thank you for your help!
Hi Khoi, all the setup does is just unpack the files into the chosen folder. So not really necessary to run it, can just copy paste the files.
Best, Vadim
Understood, thanks! A dumb question: how do I obtain those files including the executable? When I run setup on a Windows machine, it seems to create a folder which contains DiaNN.exe
. However, I don't see how to download it directly from the GitHub page. Thank you.
You need to run setup once, and then you can copy the files to any machine. No, cannot direclty download from github.
Vadim
Wanted to give an update that I used ThermoRawFileParser.exe with mono in Linux, and it worked to convert .raw to .mzML and feed into DIA-NN. Thanks!
Hi @Munchic , I hope you are doing well. I wanted to reach out about the implementation of DIA-NN on Kubernetes as a container. We are planning on doing something similar and moving away from running DIA-NN on Windows computers. Can you please help us by letting us know your implementation design and maybe the manifest files for Kubernetes? Also, thank you for giving the solution for handling thermo files which are not supported by DIA-NN Linux env at this time.
Hi @aupadh12 ! Thank you for reaching out. We implemented a cromwell WDL workflow using the Linux command line + Docker container. You can check out this code: https://github.com/broadinstitute/PANOPLY/tree/dev/third-party-modules/panoply_diann_search
Let me know if that is helpful and good luck with the Kubernetes implementation!
Hello, I get this error trying to run the linux command line version of DiaNN. I'm running Ubuntu 22.04 inside a Docker with 64 cores and 64 GB RAM. As a note, this same raw file and configuration run in the Windows GUI of DiaNN. Thank you for your help!