Hello Lance,

I've committed a fix for this issue into the next-stable branch on the 
galaxy-central repository in change set revision 9212:92c8a55a6679, so the fix 
will be included in the upcoming Galaxy release.  This fix is currently running 
on both the test and main Galaxy tool sheds as well.

You'll need to change your tool config file to use a new reserved word as 
follows:

.. image:: $PATH_TO_IMAGES/count_modes.png

This reserved word will route correctly in the tool shed when you display the 
tool inside of it's containing repository, and it will also route correctly 
when the tool is loaded from it's repository after it has been installed into 
Galaxy.  

All future tool configs that display images in the tool's help section will 
need to use this approach for tools included in repositories in the tool shed.

Thanks very much for reporting this issue, and please let me know if you run 
into any issues.

Greg Von Kuster


On Mar 22, 2013, at 1:50 PM, Lance Parsons wrote:

> Thanks for the quick response Greg.  I tried this and uploaded an update to 
> the testtoolshed and installed that in a test instance of Galaxy.  
> Unfortunately, it didn't seem to resolve the issue.  Galaxy still renders the 
> html with the image source pointing to the same location (e.g. 
> http://127.0.0.1:8080/static/images/count_modes.png).  This doesn't resolve.
> 
> You can try installing the htseq_count package from the testtoolshed to see 
> the issue for yourself. 
> 
> Lance
> 
> Greg Von Kuster wrote:
>> 
>> Hi Lance,
>> 
>> I answered this in your previous email - here's the answer:
>> 
>> To make this work in the tool shed, make the static directory that contains 
>> the image file a relative path in the tool config.  For example, your 
>> repository has the following structure:
>> 
>> htseq_count
>> htseq-count.xml
>> sam_fa_indices.loc.sample
>> static/
>>      images/
>>              count_modes.png
>> test-data/
>>      tool_data_table_conf.xml.sample
>>      tool_dependencies.xml
>> 
>> 
>> The help section of your tool config should simply use a relative path to 
>> the image file ( in this case, just a a "." in front of the path to the 
>> image file )
>> 
>> .. image:: ./static/images/count_modes.png
>>     :width: 500
>> 
>> I believe that's all that is necessary.
>> 
>> Greg Von Kuster
>> 
>> 
>> On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:
>> 
>>> For one of my tool wrappers (htseq-count) in the toolshed, I point to an 
>>> image file in the Help section.  At the moment, I'm including the image in 
>>> the repository as static/imagescount_modes.png and pointing to it in the 
>>> wrapper.xml file with ".. image:: /static/images/count_modes.png".  
>>> However, the toolshed installation doesn't copy this file to the static 
>>> directory of the galaxy install (which doesn't seem like a good idea 
>>> anyway).  Is there any way for me to include a static file and then point 
>>> to that file in the help when the tool is installed automatically via the 
>>> toolshed.. Thanks.
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___________________________________________________________
> 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:
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> 
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