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 <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> htseq-count.xml <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> sam_fa_indices.loc.sample <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> static/ <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> images/ <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> count_modes.png <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> test-data/ <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> tool_data_table_conf.xml.sample <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#> tool_dependencies.xml <http://toolshed.g2.bx.psu.edu/repository/browse_repository?id=2df7e24ce6c1f224#>


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

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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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