Problem in transfer from old to new instance

Workflow4Metabolomics Instance
1

I've got some problems when running a workflow that comes from an upload of a workflow coming from the old instance.
As I delete all mzML and dataset list of findchrompeaks I try to start the xcms wrkflow at the 1st group step using the Rdata file resulting of the merge step. But it doesn't work. In the group GUI I can't select the Rdata file.
here is the history
https://workflow4metabolomics.usegalaxy.fr/u/jfmartin/h/test-transfert-epaj
Thank's for help
Jean-Francois

2

@JFMartin have you try to edit the datatype ?

  • click on the pensil
  • select the tab Datatypes
  • in the combo list, select rdata.xcms.findchrompeaks

Your dataset should be now available for group.

3

Thank's, it works but then I've got an error because, group seems to read again the raw files mzML... :
Error in retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) :
Cannot access the sample: x3apR3.mzML located: /work/project/w4m/galaxy4metabolomics/database/files/002/196/dataset_2196646.dat . Please, contact your administrator ... if you have one!
Execution halted

So there is no other possibilities than uploading again all the raw mzML files...Too bad...
Anyway, thank's a lot for your quick response

4

Indeed, xcms need to seek complementary information within the raw data.
You will have to

  • upload them
  • use the hidden form Resubmit your raw dataset or your zip file
  • select your new dataset collection

:crossed_fingers: