Have lentivirus integration site analysis in Galaxy?

[libinglin]

Hello, are there any tools in Galaxy for exogenous gene integration site analysis, e.g. lentivirus etc.

[libinglin]

Such as the EpiVIA （GitHub - VahediLab/epiVIA: Identify vector integration site with both bulk and single-cell epigenomic assays ）from the https://doi.org/10.1073/pnas.1919259117

[jennaj]

Welcome, @libinglin

The epiVIA tool hasn’t been wrapped for Galaxy yet, but I don’t see why it couldn’t (or did I miss a licensing restriction?).

Below is how to make the request. I’m sure the UPenn researchers are aware of Galaxy, so reaching out to both them and the IUC and cross-linking the tickets seems like a good way to gather more support and coordination around this project.

@jennaj

Where to make the next request

1. Open an issue at the target tool’s development repository and make the request as “Wrap for Galaxy”.

or

2. Start the request at the IUC instead. GitHub - galaxyproject/tools-iuc: Tool Shed repositories maintained by the Intergalactic Utilities Commission

and

3. The third option is to wrap the tool yourself and collaborate with the two groups above.

Most of the work done for Galaxy is provided by community contributors, and the attribution procedures are very good. This includes not just the technical/coding parts, but the wrapper design (which parameters, how to model them) and scientific review (potential new tutorials, help content on the form).

If you would like to start up the discussion with the IUC to see if anyone has explored this tool already or not, or if there are any current plans I didn’t find, you can reach them at their chat. Find the link at their repository above.

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The remainder of the bioinformatics tools/manipulations are already available in Galaxy from what I can tell – so creating a workflow shouldn’t be a trouble. You will just need this new part added which performs the BWA alignment sorting.

Hope this helps! If there is another tool that someone knows about that is already in Galaxy, please feel free to correct me and offer other pointers