I have an online account in galaxy where i am trying to work with an example dataset. I can see tophat hat in the list of tools on the left but count not find tophat2. Previously, when working with the same data set I have used tophat2 and now , when I am trying to repeat the analysis, i dont find tophat2 in the list. Could someone help to add tophat 2 to my tools list. Also, can someone explain me why this appears and disappears at times.
The tool is just named "Tophat" now. If you are ever unsure about the version of wrapped 3rd party tools, on the tool form click on the top right menu "Options -> See in Tool Shed" to view the repository (where version information is noted). And after running, the version information is noted on the "i" info form (per dataset/job).
If you need to re-run "Tophat for Illumina" for some reason, it is still on Main, but hidden at this time, as that tool version tool has been deprecated. Use the "re-run" button from a prior "Tophat for Illumina" job for now to access it. Or, if you had it in a prior Workflow, it will still execute from there.
We are updating/replacing tools and will be working out a strategy to making using any hidden tool versions easier to access through the primary UI.
Thanks, Jen, Galaxy team