How to run MiXCR or AIRR-seq analysis

usegalaxy.org support
1

Hi. I would like to analyze B cell receptor (BCR) and T cell receptor (TCR) recombination data on Galaxy. In the past I have used MiXCR via the command line.

To use MiXCR, do I need to install the tool from the toolshed (something I do not yet know how to do), or install via conda or something? Thank you in advance!

2

Hi @Patrick_Collins
Only server admins can install tools. Ping @jennaj - a tool installation request for the ORG server.
I checked MiXCR in the main tool shed: it was last updates in 2019, nearly five years ago. Unmaintained tools usually accumulate incompatibilities with constantly evolving Galaxy environment, making installation somewhat complicated. Let’s wait for reply from the ORG people.
Kind regards,
Igor

3

Hi @Patrick_Collins and @igor

It seems to be restricted with a license. The IUC removed the development repository, too, so I can’t find out who worked on it originally.

Now, sometimes we are able to add in an extra confirmation button about “academic use” when hosting licensed tools at the public servers but that does only work if everyone agrees… Maybe that could be revisited by contacting the original tool author.

So, the options are one of these as far as I know

  1. Set up a local Galaxy server and attempt to install directly from the ToolShed. But review the ticket below, it seems someone else had problems with it and I don’t think it was resolved. Could be a data/parameter issue OR some bugging behavior, and the latter could be complicated for the reasons Igor described.
  2. Use the tool directly, outside of Galaxy. You could export your Galaxy data files, run that tool, then import the results back to Galaxy for data interpretation steps.

XRef

Not a very satisfying answer but I can’t think of another solution for this tool specifically.

4

Thanks @igor and @jennaj. It seems like the best choice is to use outside Galaxy. Appreciated

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