using Qiime2 in Galaxy

Hi everyone, I am trying to learn to use QIIME2 in Galaxy. I have already analysed my data in the original QIIME2 but want to learn Galaxy anyway. I cannot figure out how to import the data at all even after following the tutorial. I think it might be that the tutorial is for Casava One Eight Single Lane Per Sample Directory Format whereas mine is manifestPhred 33. Does anyone know how to do this? It is very frustrating not knowing what is wrong after following the tutorial.

I have asked on the Galaxy forum and they have been very helpful on there but also suggested asking here.

Best wishes

Hello @Mantella86. You can't import an artifact using a manifest format in q2galaxy because manifest files as a concept don't make sense in galaxy (galaxy doesn't really do things in terms of filepaths, and has its own ways of solving the problems manifest files are supposed to solve); however, you do have some other options.

The simplest work around would be to import your artifact as normal on your local machine and then upload the already imported artifact to galaxy. You can do that pretty easily using the upload data tool on galaxy, but let me know if you need any help with that.

If that isn't an option for you, there are workarounds, but they are a bit more involved. If you need to upload your raw data to galaxy and import it in galaxy, I'll need to know if your data is single or paired end.

Hi Oddant1, Mine are paired end sequences. I have been following this tutorial on data import into Galaxy Importing demultiplexed sequence data — QIIME 2 Cancer Microbiome Intervention Tutorial

The tutorial shows you how to import a copy and pasted table from URL. I didn't do that I just uploaded normally.

I have tried to pair my paired end sequences (circled in blue) that didn't work and I tried uploading the paired end sequences and creating a list just like in the tutorial (circled in black) the tutorial data is circled in red and that didn't work either.

I have however successfully uploaded my metadata into a qsv format for QIIME.

I have no idea what else to try. I hope someone has some experience in this.

Kind regards

What you're going to need to do is rename your files to match the casava format and import them as the casava fromat. I've used the tutotial data found here for this examples.

Step 1: rename your files to match the following regex: .+_.+_R[12]_001.fastq.gz

Step 2: Upload your data to galaxy as a collection of type list

Step 3: Build the collection

Step 4: Import the collection

Let me know if you need any clarification on any of these steps.

Thank you, that worked well :slight_smile: . Do you know why it will not accept my silver taxonomy or sequence file though? I want to to the classification and then export in the form of a tsv file so I can go through the community analysis in R. It just keeps telling me ' unable to finish job' upon uploading.

You're saying that failure is happening when you try to upload the already imported .qza? If you click on the bug icon or the ! icon beneath the "Unable to finish job" message is there any information on either of those pages?

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