After upgrading to the latest version of FASTQC (0.11.7 to 0.11.8) the HTML files cannot be viewed in browser. Is there a fix available ?
is this a Galaxy qquestion? The Galaxy Tool wrapper for FastQC is currently at version 0.72+galaxy1 (and wraps FastQC 0.11.8). How exactly did you upgrade FastQC?
Hi - You will need to set some admin permissions for viewing the HTML output. This is set by tool and version.
In the Galaxy UI, go to
Admin > Tool Management > Manage whitelist and check off the updated FastQC tool version. I can’t remember if this requires a restart or not, so if it doesn’t seem to work after, restart and all should work.
Update: Does NOT require a server restart
Update – if you were working at Galaxy Main https://usegalaxy.org, I just whitelisted the tool there as well (
Tool: **FastQC** Read Quality reports (Galaxy Version 0.72+galaxy1). It was recently updated and that last step was missed. Fixed now.
AND – it turns out that a server restart is not needed. Any “whitelist” changes take effect immediately.
If you are running
FastQC line command, then this isn’t the right place to ask for help as @wm75 notes in his reply. You can try the contact here https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ or search other general bioinformatics Q&A forums.
Thanks, this workaround works on my local Galaxy installation.
Yes, it is a Galaxy question. The responses provided by jennaj below resolved the issues on the Galaxy Main and Galaxy local installations.
Super, glad this worked out both places