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BiAPoL / blog

Most of us study and work at the Bio-image Analysis Technology Development group at the DFG Cluster of Excellence “Physics of Life” at the TU Dresden. We blog about image data science, knowledge exchange and research data management in the life sciences.
https://biapol.github.io/blog/
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Add new blog post about Elephant installation windows #78

Closed stefanhahmann closed 3 months ago

stefanhahmann commented 5 months ago

Recently, I was involved installing ELEPHANT server on 2 end users windows machines. I collected what I have learned from that and would like to share it via this blog post for further reference.

jo-mueller commented 4 months ago

Hi @stefanhahmann ,

I just tried the installation and unfortunately didn't get past the integration of wsl and docker desktop. Do you use it on a TU Dresden laptop? I think my issue is, that I have to run docker-desktop as administrator (because of docker being docker, I suppose), but the wsl is configured for my personal user, so that docker-desktop never gets to discover it, although it's properly installed.

Is there a way to install it without admin privileges? How did you do it on your windows machine?

edit: I just tried it with Podman and I get to the point where I can pull and build the container from the command line. The entrypoint scripts seem quite docker specific, though :S

stefanhahmann commented 4 months ago

Hi @stefanhahmann ,

Thanks for testing this through.

I just tried the installation and unfortunately didn't get past the integration of wsl and docker desktop. Do you use it on a TU Dresden laptop? I think my issue is, that I have to run docker-desktop as administrator (because of docker being docker, I suppose), but the wsl is configured for my personal user, so that docker-desktop never gets to discover it, although it's properly installed.

This is an interesting catch. I use it on a TU Dresden laptop. Are you starting Docker Desktop with your personal user or with the administrator user? Both should be possible, but leads to different behavior of docker. Starting docker as personal user should provide the wsl that you have installed as personal user.

Is there a way to install it without admin privileges? How did you do it on your windows machine?

While running the docker installer, the installation program asks for an administrator to confirm the installation. Running docker should however be possible without administrator right, afaik.

edit: I just tried it with Podman and I get to the point where I can pull and build the container from the command line. The entrypoint scripts seem quite docker specific, though :S

Yes, the entry point script assumes docker.

jo-mueller commented 3 months ago

Hi @stefanhahmann ,

I went through the installation and it ran alright :) I'd have one question about the part of running it in the end, though: I installed the Mastodon plugin in FIji by enabling the ELEPHANT/Mastodon/Mastodon DeepLineage update sites. I then open the Mastodon plugin in Fiji from Plugins > Mastodon but I don't see the same window as in the blog post:

Capture

stefanhahmann commented 3 months ago

Hi @stefanhahmann ,

I went through the installation and it ran alright :) I'd have one question about the part of running it in the end, though: I installed the Mastodon plugin in FIji by enabling the ELEPHANT/Mastodon/Mastodon DeepLineage update sites. I then open the Mastodon plugin in Fiji from Plugins > Mastodon but I don't see the same window as in the blog post:

Thanks for spotting this. In fact, the text was not specific enough here. You have to open a Mastodon project and only then the Elephant client will be shown.

I updated the blog post regarding this.