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
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. - Nik. On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi <najoshi@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
-- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA
Hi, What extension were you working on? Something that's available on the tool shed [1]? :) ... I'm looking into displaying some images from some analyses as well, and would be interested to have a look at the code. Cheers // Samuel [1] http://toolshed.g2.bx.psu.edu/ 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.
- Nik.
On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi <najoshi@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
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 the toolshed). Make sure to have the html sanitize option OFF in your universe_wsgi.ini file. Alex ________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Samuel Lampa [samuel.lampa@gmail.com] Verzonden: woensdag 19 december 2012 12:46 To: Nikhil Joshi Cc: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] producing HTML output with images Hi, What extension were you working on? Something that's available on the tool shed [1]? :) ... I'm looking into displaying some images from some analyses as well, and would be interested to have a look at the code. Cheers // Samuel [1] http://toolshed.g2.bx.psu.edu/ 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.
- Nik.
On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi <najoshi@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Ah, it turned out that "Galaxy ToolFactory" was the answer to my needs: https://bitbucket.org/fubar/galaxytoolfactory Best // Samuel On 12/19/2012 12:46 PM, Samuel Lampa wrote:
Hi,
What extension were you working on? Something that's available on the tool shed [1]? :)
... I'm looking into displaying some images from some analyses as well, and would be interested to have a look at the code.
Cheers // Samuel
[1] http://toolshed.g2.bx.psu.edu/
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.
- Nik.
On Thu, Feb 16, 2012 at 8:15 PM, Nikhil Joshi <najoshi@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
participants (3)
-
Bossers, Alex -
Nikhil Joshi -
Samuel Lampa