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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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SignalP tool fails to install #78

Closed tothuhien closed 1 year ago

tothuhien commented 1 year ago

A user reported that a job of SignalP did not start from Saturday, with message "The job is waiting to run". The tool hasn't been run before, so there may be problem with the installation.

tothuhien commented 1 year ago

The tool requires 'signalp' package which is only available in 'predector' Conda channel. Maybe it's not one of the default conda channels?

kjetilkl commented 1 year ago

The "signalp" package in the "predector" channel is a bit strange. Even if you install it via Conda, you still have to download "signalp" as a tarball from the original web site and then use a script in the Conda package to register your installation and unpack the tarball. I think this has to do with the license of the program, since you have to fill in your name and affiliation and check off "I agree" on the license agreement when submitting a request to download it. This will send you a temporary URL by email, which you can then use to access the actual files. So, even if we had added the "predector" Conda channel in Galaxy, the automatic container build step would still have failed.

I am trying to build this container manually instead. The same tool suite also includes a few other tools, and I will try to include their dependencies in the container as well. So far, it is not going too well :-/

kjetilkl commented 1 year ago

Well, this has certainly been an exciting, weeklong trip into the dark pits of dependency hell. I belive I have fixed SignalP now, and also 4 other tools in the same suite: Promoter 2.0, TMHMM 2.0, RXLR Motifs and WoLF PSORT. For the last tool, psort, I think I have managed to install all the dependencies into the container, but it fails with some Perl issues. Unless someone actually needs to run psort, I will just leave it as is for now rather than waste more time on it.

tothuhien commented 1 year ago

Thanks @kjetilkl , I will inform the user about this 👍

sveinugu commented 1 year ago

Well, this has certainly been an exciting, weeklong trip into the dark pits of dependency hell.

Sorry to hear about that. I hope you have emerged on the other side relatively sane. Best wishes for your recovery - I do think your scars will heal eventually! 🤕