Entering edit mode
7.8 years ago
matthew.ford
•
0
Hi,
I have been using tophat version 2.1 on the online server recently and it has been working well. However tophat has started to produce empty files with the following error message:
Log: tool progress Log: tool progress /galaxy-repl/main/jobdir/013/266/13266476/tool_script.sh: line 9: tophat2: command not found
I have tried many different files and some old files which have worked previously but I am still running into the same problem. Any advice on what might be going on would be great because at the moment I am a bit stumped....
Best,
Matt
Looks like you are running tophat through a local galaxy mirror. You should contact the local galaxy admins and point out the error to them.
Really that's odd. I definitely wasn't aiming to be running through a local mirror. Is it possible to change to using the online server as I know our local galaxy is out of data?
Not clear if your are or are not using a local mirror at your institution? Do you use http://usegalaxy.org for Galaxy or some other URL? If latter, then you are likely using a local mirror.
If you are using a local galaxy mirror then there is no way to switch your jobs to Galaxy @PSU (http://usegalaxy.org). You would need to upload your data there and then run the jobs.
I am running all my jobs at https://usegalaxy.org/ so I guess it is not a local mirror issue...
It would be best to post this question at Biostar dedicated for Galaxy @PSU: https://biostar.usegalaxy.org/ This would make sure that this error reaches the admins at PSU galaxy.
Will do. It seems to be a problem with that version of tophat as if I run it on an older version it seems to work.
For future reference use
ADD REPLY/ADD COMMENTbuttons when providing additional information or responding to a pre-existing comment. SaveSUBMIT ANSWERfor a real answer for the original question.If the empty results are showing up as green in the history, then please do post on the Galaxy biostars. They monitor the site and can then look through your history to debug the issue (give them enough info to figure out what your username is on the main Galaxy server).
N.B., the reply time might be a bit longer than normal. Almost the entire Galaxy crew as at a conference this week and they're pretty...busy with it.
Multiple people appear to be having this problem over at Galaxy biostars: https://biostar.usegalaxy.org/p/18247/ which is where @matthew added his note.
Lovely. If someone could share their history with Jenn then they could get things resolved.
@matthew.ford: Please share your broken history with her. If you don't get a reply in the next day or so then mention that in this thread and I'll pester the Galaxy folks into looking into the problem.
Edit: I see someone has posted their history :)
Edit2: Ah, the tool dependency package is broken or there's something not being moved over to the jetstream cluster (the Galaxy main clustering stuff is crazy complex).