Hi, I am novice to RNA-Seq Analysis and Galaxy server. Currently am running a work-flow of 40 steps (tuxedo) in Galaxy server. A tophat output has a metadata error showing "yellow color" and this dataset will be the inputs in further workflow steps. The problem is that I can't changed it nor "auto-detect" option is not working. Is there any possibility to change the metadata without disturbing the workflow. Thanks in advance.
Try updating the metadata now. Tophat "accepted hits" datasets are known to have metadata issues (from the Jetstream cluster only, last time I checked). Auto-detect is how to fix this problem. Do this before running downstream tools. It may mean that you need to split up your workflow into two - 1) before and up through Tophat 2) after Tophat.
Or pick a different specific cluster with the "Job Resource Parameters" option on the tool form and rerun (a rerun is not a bad idea anyway, as the server has been updated recently, resolving some known issues). The default Galaxy cluster and TACC Stampede (beta) are valid alternatives to Jetstream, the others are for testing and can produce failed jobs for various reasons - so should not be used).
If this does not resolve the problem, send in a bug report from an error dataset (any) and note the problematic Tophat dataset by number. Make sure it is not deleted. Or send in a link to the shared history with the same information directly to email@example.com. Both are sent to the same internal list, so your data privacy is protected. Also please include a link to this post in the email/bug report comments so we can link the two. This assumes you are working at http://usegalaxy.org or can reproduce the problem there.
Thanks! Jen, Galaxy team