CutAdapt adapter file in Galaxy workflow


I am the admin for the Galaxy instance that we use at our institution, which is connected to a High-performance cluster as well. I have developed an RNA-Seq Primary analysis workflow and have incorporated “CutAdapt” tool. It works perfectly but I want to add my own list of adapter sequences. The user can provide their own list but I would like to have this available to them instead of them having to upload their own adapter sequence file. Is there a way that this file can be provided and the user can select this file from a drop-down list? I have made a tutorial for this and I don’t want the users be bogged down by uploading too many files (especially first-time users). Could you help me with getting a file available to all users of the instance?

Thank you for reading, I appreciate any suggestions!

Hi @Priyanka_Bhandary

There are two ways to do this:

  1. Put the adaptor file in a Data Library on your server, then show people how to get data from there in your tutorial. Data copied from a library doesn’t consume any quota space for the user, so there are many use cases for this.

  2. Figure out how to add in the custom adaptors directly. I’m not exactly sure how this is done, and the public sites don’t add them in (or did I miss it?) … but seems possible. The “dummy adaptors” seem like a placeholder for custom files, so maybe review there first. It might be hardcoded into the tool wrapper but you can adjust that on your own server of course. Galaxy | Tool Shed

Thank you @jennaj, I think we will move forward with using the data libraries. Thank you for your detailed answer!

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