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

___________________________________________________________ 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/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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

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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- 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: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/