Have a look at the wiki there is a step-by-step example if I remember correctly.
Furthermore, another tool which uses this kind of output is the fastQC tool (available in
Make sure to have the html sanitize option OFF in your universe_wsgi.ini file.
Van: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] namens
Samuel Lampa [samuel.lampa(a)gmail.com]
Verzonden: woensdag 19 december 2012 12:46
To: Nikhil Joshi
Onderwerp: Re: [galaxy-dev] producing HTML output with images
What extension were you working on? Something that's available on the
tool shed ? :)
... I'm looking into displaying some images from some analyses as well,
and would be interested to have a look at the code.
On 02/17/2012 05:33 AM, Nikhil Joshi wrote:
Well, I guess I figured it out... it turns out that galaxy does some
internal magic to automatically add the path of the output directory
to the filename when it is rendering the html. So what I needed to do
was to create the file in the temporary job directory and then just
use the file name without any path information in the html and galaxy
does the rest. If anybody has any other advice or pitfalls to avoid,
please feel free to let me know.
On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi <najoshi(a)ucdavis.edu> wrote:
> Hi all,
> I am having trouble producing HTML output with images. In the past I
> have been able to produce HTML files with no images and it seemed to
> work fine. However, now I am writing a script that produces
> diagnostic images and I want to display all of the images on one page
> using HTML. I am using the "files_path" variable to create the plots
> in the working directory, and then I am using the "extra_files_path"
> variable to access the final plot from the html file. I look at the
> resulting HTML files and it points to the proper plot full path, and
> the plot DOES exist... but when I click to view the output, the plot
> doesn't render. It just shows an empty box with a "broken image"
> icon, however, the text does render. I copy the plot file, and I can
> view it fine by itself. I copy the plot and the html and I can view
> the page just fine offline, but galaxy doesn't want to render the
> image for some reason. What am I doing wrong?
> - Nik.
> Nikhil Joshi
> Bioinformatics Programmer
> UC Davis Genome Center
> Davis, CA
Developer at SNIC-UPPMAX www.uppmax.uu.se
Developer at Dept of Pharm Biosciences www.farmbio.uu.se
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