Missing tools and running local Galaxy instance on Windows 10

usegalaxy.org support
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#1

Hello,
I have been trying to create a protein database from RNA-seq files on the usegalaxy.org server. There are a few tools required for this workflow that are missing on the server. I tried using the EU server where the tools are present but the upload has been taking ages.
I also tried to create a local galaxy server but since I have Windows 10, I have been getting one error after another.
My last option is to try a dual boot but I wanted to check if there is an easier way of getting the tools added to the usegalaxy.org server. The tools are: 1 CustomProDB, 2.Convert gffCompare annotated GTF to BED, 3. Translate BED transcripts cDNA in 3frames or CDS, 4. bed to protein map, and others under Creating FASTA Databases mentioned here- https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html#translate-transcripts
Also, if anyone knows any other way to create a local Galaxy server on Windows 10 apart from using the dual boot method, I would appreciate the information (I have tried using python 3.6 and Ubuntu but it did not work for me).

Thank you and Happy Holidays
Lee

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#2

Hi there, unless you are an OS expert I do not recommend trying to run Galaxy on Windows, it is not supported. Your best bet for testing Galaxy out locally is to run a linux virtual machine using software like the virtual box and an OS image of e.g. ubuntu .

Alternatively you can choose to be more patient with usegalaxy.eu uploads, they will finish eventually. You can also obtain a disposable linux server from e.g. AWS or other cloud provider. There is also a docker image available on the training page you shared, which you can install on Windows too I believe.

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#3

I’ve been running Galaxy on Windows Subsystem for Linux which was mostly working okay except that some eggs randomly failed to installed. With WSL2 it should hopefully work better (instructions for installation: https://docs.microsoft.com/en-us/windows/wsl/install-win10)

The instructions for how I got it to run last year were uploaded here: https://galaxyproject.org/admin/config/windows/

From the way you describe your issue I am however wondering if this is really what you really want to do. Setting up your own Galaxy server should in most cases not be faster than uploading your files from one Galaxy server to another, if you share your history and make all objects available (click the cog wheel to the right above your history pane to find the share history option), then you can just right click the save file icon for each dataset you want to copy to get the URL to the data and then paste it into the file uploader on usegalaxy.eu to load data directly from usegalaxy.org to usegalaxy.eu.

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