FastQC HTML file not visible when using Galaxy hands-on training

usegalaxy.org support
1

I was working on usegalaxy.org

I started working through the Galaxy training/Sequence analysis/Quality control hands-on training on Friday, July 12. At the time I had no problems. However, today (Tue, July 16) when I returned to the history and tried to view the results for ‘FastQC on data_1:Webpage’ I didn’t see any of the graphical displays.

The green box underneath the step name contained: ‘Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/024/239/24239388/_job_tmp -Xmx7g -Xms256m.’

When I clicked on the icon to view details and then on ‘stderr,’ it displayed the same message: 'Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxyrepl/main/jobdir/024/239/24239388/_job_tmp -Xmx7g -Xms256m

I am wondering if something needs to be reset as described in the response to a similar message 5 days ago ‘FastQC file not visible - Add tool to HTML display “whitelist”’

Thank you!

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2

exactly, thanks for the report, I think I fixed it now for good (until the next version of fastqc comes out :D)

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