Conda error XSeeker preparator tool

Galaxy
1

Hi @team.galaxy

We have an issue with XSeeker Preparator tool on usegalaxy.fr " Conda dependency seemingly installed but failed to build job environment."
Any clue?

Thanks
Yann

2

There are 2 tools xseeker_preparator and the two don't have merged conda environnement.
Galaxy try to stack 11 separate env and should fail.

@fgiacomoni and @yguitton, you should review the compatibility between dependencies of this tool :confused:

My advise is to fix the main package and let Conda find the version that match for the other ones.

For example, you fix bioconductor-camera. Conda will list the all the packages with their versions.

conda install -n test bioconductor-xcms bioconductor-camera==1.48.0 git r-blob r-dbi r-fst r-optparse r-stringr r-purrr r-rsqlite r-dbmodelr

My 2 cents

3

Thanks Gildas, good idea. I'm going to try that and resubmit tool on main TS.
F

4

I pushed a new version of the tool of main TS under [1d91c4600466] version.

5

Hi @yguitton

The new version of the tool is installed :

6

@yguitton did you test the new version ? thank you and have a good spring break !

7

@fgiacomoni , I ran my tests on https://usegalaxy.fr/. After Camera 1.48, the Xseekerpreparator step is OK. But I have errors on Xsseker, impossible to draw KMD or 2D plots without error. "cluster_sample is not a valid field or method name for the reference class "ORM"

any clue on your side?
Yann

8

Hi Yann, may you share your history with me and Lain ! Thank you !

9

Hi @fgiacomoni @Lain
Here is the link Galaxy | France | Accessible History | Xseeker_oneClass

Yann