Hi Christopher!
Dear Björn,
I just installed Salmon on our Galaxy instance and I have a couple of basic questions.
Sure, thanks for getting in touch!
Currently the reference transcriptomes are put in the same data table as the genomes, would it be of interest to separate this and give the
transcriptomes their own table? I could probably try to do this...
That I don't understand? Salmon is using this one here, isn't it? https://github.com/bgruening/galaxytools/blob/master/tools/salmon/salmon.xml...
There is a data manager available that unfortunately has a bug. We fixed that and it now populates the reference genome data table.
Do you mean this one? https://github.com/ieguinoa/data_manager_salmon_index_builder
I would probably modify this as well use the new table. Could this be useful? I'm not sure how to proceed...would I give you the modified Salmon wrapper for inclusion in the package?
If you can, please feel free to create PRs to the repositories, so we can all reviewed it. And then, when we merge, it gets automatically updated to the Tool Shed :) Thanks! Bjoern
Best regards,
Christopher
-- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician
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