Hello Peter Thanks for the fast response. From reading around elsewhere I'd understood that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and it didn't seem to help. But I might have missed something, so I'd be interested to know if it works for you. Best wishes Peter On 09/08/17 14:57, Peter Cock wrote:

It looks like something important is not showing in the best practise website, special variable $PATH_TO_IMAGES as per the linked example:

.. image:: $PATH_TO_IMAGES/slop-glyph.png

Let me look into this,

Peter

On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

...

Dear devs

I've been updating the <help> section for a locally developed tool and want to include some images, but I've had some issues trying to see them when testing locally.

I've followed the instructions outlined here:

https://github.com/galaxy-iuc/standards/blob/master/docs/best_practices/tool...

(i.e. put the images files into a 'static/images/' subdir of the tool directory and reference them using ".. image:: picture.png")

However when I load the tool into a Galaxy using "planemo serve ..." the images fail to render: I just get a line of text with the image filename. The same thing happens when I add the tool manually on our local server (i.e. by adding a <tool file=...> reference to the tool XML in the appropriate conf.xml file).

If I upload the same tool files to a toolshed and then install from there, I do see the images rendered correctly.

I'm a bit baffled as to why there should be a difference. Is there an option or setting I've missed to turn on the image rendering for non-shed-installed tools? Or have I made some other mistake?

Thanks for your help,

Best wishes

Peter

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/

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

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

There is an open issue for these paths not working with vanilla Galaxy tools https://github.com/galaxyproject/galaxy/issues/1676. -John On Wed, Aug 9, 2017 at 10:03 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

I'm puzzled now too, cross reference

https://github.com/galaxy-iuc/standards/pull/46

and the original:

https://github.com/galaxy-iuc/standards/issues/12

Peter

On Wed, Aug 9, 2017 at 3:01 PM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

...

Hello Peter

Thanks for the fast response. From reading around elsewhere I'd understood that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and it didn't seem to help. But I might have missed something, so I'd be interested to know if it works for you.

Best wishes

Peter

On 09/08/17 14:57, Peter Cock wrote:

...

It looks like something important is not showing in the best practise website, special variable $PATH_TO_IMAGES as per the linked example:

.. image:: $PATH_TO_IMAGES/slop-glyph.png

Let me look into this,

Peter

On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

...

Dear devs

I've been updating the <help> section for a locally developed tool and want to include some images, but I've had some issues trying to see them when testing locally.

I've followed the instructions outlined here:

https://github.com/galaxy-iuc/standards/blob/master/docs/best_practices/tool...

(i.e. put the images files into a 'static/images/' subdir of the tool directory and reference them using ".. image:: picture.png")

However when I load the tool into a Galaxy using "planemo serve ..." the images fail to render: I just get a line of text with the image filename. The same thing happens when I add the tool manually on our local server (i.e. by adding a <tool file=...> reference to the tool XML in the appropriate conf.xml file).

If I upload the same tool files to a toolshed and then install from there, I do see the images rendered correctly.

I'm a bit baffled as to why there should be a difference. Is there an option or setting I've missed to turn on the image rendering for non-shed-installed tools? Or have I made some other mistake?

Thanks for your help,

Best wishes

Peter

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/

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

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

---

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: https://lists.galaxyproject.org/

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

An update: looking some more, it appears that the <img> tags produced by both 17.01 and 17.05 are the same (i.e. in both cases there is no prefix). So the "missing" prefix is not the reason for the problem in the later release, as I'd originally thought. In fact with the help of git bisect, as far as I'm able to tell the problem seems to be associated with changes in commit id 6e32b0f7c119ca6c3d54a761e64f49fe6a7f8280: https://github.com/galaxyproject/galaxy/commit/6e32b0f7c119ca6c3d54a761e64f4... and specifically those associated with the file 'static/scripts/bundled/analysis.bundled.js'. Unfortunately I'm not able to make much sense of the diff, or to identify which parts might be relevant to this problem. I suppose it's possible that the problem only manifests when these changes interact with something elsewhere in another commit. Once again any help or suggestions would be appreciated, thanks! Best wishes Peter On 21/08/17 16:36, Peter Briggs wrote:

Dear devs

The rendering of images in tool XML 'help' sections is broken for release_17.05 when serving Galaxy from a subdirectory using proxy-prefix.

The <img...> tags are rendered in the tool helps but point to relative URLs which don't include the prefix (e.g. "admin_toolshed/static/images/756ced91f537cdf0/norm_IGVsnapshot_indFiles.png" rather than "<PROXY_PREFIX>/admin_toolshed/static/images/756ced91f537cdf0/norm_IGVsnapshot_indFiles.png").

I've looked at the Galaxy code but so far I haven't been able to see where these tags are generated (nor whether the proxy prefix is even available to the Galaxy webapp).

This problem doesn't appear to be in release_17.01 (i.e. images display regardless of proxy-prefix), but it is still present in the 'dev' branch. I believe it's independent of the PATH_TO_IMAGES issue raised previously.

Can anyone suggest any starting points for looking into how to fix this?

Thanks for your help - I really like to get this fixed as it's breaking the very useful inline documentation for e.g. 'deepTools', as well for a locally developed tool we're currently trying to roll out on our production instance.

Best wishes

Peter

On 10/08/17 16:12, John Chilton wrote:

...

There is an open issue for these paths not working with vanilla Galaxy tools https://github.com/galaxyproject/galaxy/issues/1676.

-John

On Wed, Aug 9, 2017 at 10:03 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

I'm puzzled now too, cross reference

https://github.com/galaxy-iuc/standards/pull/46

and the original:

https://github.com/galaxy-iuc/standards/issues/12

Peter

On Wed, Aug 9, 2017 at 3:01 PM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

...

Hello Peter

Thanks for the fast response. From reading around elsewhere I'd understood that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and it didn't seem to help. But I might have missed something, so I'd be interested to know if it works for you.

Best wishes

Peter

On 09/08/17 14:57, Peter Cock wrote:

...

It looks like something important is not showing in the best practise website, special variable $PATH_TO_IMAGES as per the linked example:

.. image:: $PATH_TO_IMAGES/slop-glyph.png

Let me look into this,

Peter

On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

...

Dear devs

I've been updating the <help> section for a locally developed tool and want to include some images, but I've had some issues trying to see them when testing locally.

I've followed the instructions outlined here:

https://github.com/galaxy-iuc/standards/blob/master/docs/best_practices/tool...

(i.e. put the images files into a 'static/images/' subdir of the tool directory and reference them using ".. image:: picture.png")

However when I load the tool into a Galaxy using "planemo serve ..." the images fail to render: I just get a line of text with the image filename. The same thing happens when I add the tool manually on our local server (i.e. by adding a <tool file=...> reference to the tool XML in the appropriate conf.xml file).

If I upload the same tool files to a toolshed and then install from there, I do see the images rendered correctly.

I'm a bit baffled as to why there should be a difference. Is there an option or setting I've missed to turn on the image rendering for non-shed-installed tools? Or have I made some other mistake?

Thanks for your help,

Best wishes

Peter

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: https://lists.galaxyproject.org/

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

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

---

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: https://lists.galaxyproject.org/

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

-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482