Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did
give the proper output. Furthermore, FastQC generating the proper output when I
run it from Galaxy. However, Galaxy is having trouble accessing the files. If I
go into the filesystem, I can find all of the files in
I ran FastQC on the Penn State public instance, and it gives HTML output with
pictures in-line and all of the linked files accessible. When I mouseover the
link, it looks the same as it does on my local instances, in that the address
is in the following format:
[Galaxy web address]/datasets/[16 character hash]/display/[filename]
Knowing what's going on "under the hood" would be extremely helpful towards my
troubleshooting. So far I can't find anything interesting in paster.log, nor in
the Apache log files.
From: Ross [mailto:ross.laza...@gmail.com]
Sent: Wednesday, June 06, 2012 6:07 PM
To: Dorset, Daniel C
Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC
The wrapper doesn't introduce any new dependencies other than a working FastQC
install in the right place so can you please let us know what happens when you
run FastQC from the command line as the user running your Galaxy processes - it
should start an interactive FastQC session where you can try running a real
fastq input and check that you get the HTML outputs.
Once it's all working from the command line, try the tool again and let us know
how that turns out please?
On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C <daniel.dor...@vanderbilt.edu>
> I'm running two separate instances of Galaxy on two different servers.
> On both servers, whenever I run FastQC, I can see the result HTML
> file, but none of the pictures show up. Furthermore, if I try to
> access the links at the bottom of the page, they don't lead to any real files.
> If I look in my database/files/subfolder, I see a dataset_### file
> that contains the HTML info, which I am able to see in Galaxy. There
> is another folder named "dataset_###_files," and all of the pictures
> and the FastQC results zip file are contained in there. I can access
> them with full read permissions, and the sizes appear correct.
> Has anyone else experienced this problem?
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Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School; Head, Medical Bioinformatics,
BakerIDI; Tel: +61 385321444;
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