I am running qiime2 in galaxy. I have uploaded my sequence files to galaxy and created a collection to import them using qiime tools import, with the SampleData(PairedEndSequencesWithQuality) in Casava18 format. Usually it would identify the collections available in your History but in this case it doesn’t do it. I tried doing it in native installation in MacOS terminal and it imports the sequences using the same tools and format and it creates a demux.qza file that I can readily upload in galaxy and continue the analysis without an issue. Has any body had a similar experience?
This sounds like an issue with Galaxy. Maybe the folks on the Galaxy forums would have better advice! https://help.galaxyproject.org/
That's great to hear! You can safely mixed and match local analysis on a computer and 'cloud' analysis on Galaxy servers because it's the same Qiime2 in both places.
@colinbrislawn great! I used qiime2 in galaxy/eu because they do not time you out when running long processes. I tried denoising sequences files that had an unusually high number of reads natively, in the galaxy US one and in the cancer galaxy, I even tried it on a local HPC, and everytime it timed me out. Thanks for your help again. Fernando