When I use HISAT2, it fails with the error message: cannot find 'read_f'. I used it at the beginning of the week and it worked properly. I saw that it had been updated. Is the error due to this update?
Galaxy main has been undergoing some major upgrades this week (as noted in the banner at http://usegalaxy.org). However, I have not seen this particular error yet reported.
Two choices:
Wait until the banner is removed, then re-run the job. If it fails, send in a bug report. I cannot give a firm time estimate for when this would occur right now.
Send in a bug report now from the error dataset. Please make sure the inputs and error dataset are undeleted. Also try to limit the size of the history to just include the key datasets (copy these into a new history if needed as very large histories are difficult to review). Include a link to this Biostars post in the comments so that we can link the two. We can use your example to eliminate certain known issues, investigate and report new ones, use it for testing if/when a fix is needed, and to provide you with more feedback (generalized feedback we will post back here as an answer for others that may have run into the same issue). I didn't see a bug report already - but perhaps your Galaxy account and user name here at Biostars differ.
Thanks and I will watch for a bug report in case you decide to send one in. Jen, Galaxy team
Which version are you using?
I am using it on the main Galaxy, Galaxy Version 1.0.1