Image in tool XML "help" section only renders when installed from toolshed?

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Image in tool XML "help" section only renders when installed from toolshed?

Peter Briggs
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_xml.rst#including-images

(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 [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: Image in tool XML "help" section only renders when installed from toolshed?

Peter Cock
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
<[hidden email]> 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_xml.rst#including-images
>
> (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 [hidden email]
> 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/
___________________________________________________________
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/

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Re: Image in tool XML "help" section only renders when installed from toolshed?

Peter Briggs
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
> <[hidden email]> 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_xml.rst#including-images
>>
>> (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 [hidden email]
>> 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 [hidden email]
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/

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Re: Image in tool XML "help" section only renders when installed from toolshed?

Peter Cock
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
<[hidden email]> 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
>> <[hidden email]> 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_xml.rst#including-images
>>>
>>> (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 [hidden email]
>>> 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 [hidden email]
> 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/
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Re: Image in tool XML "help" section only renders when installed from toolshed?

John Chilton-4
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 <[hidden email]> 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
> <[hidden email]> 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
>>> <[hidden email]> 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_xml.rst#including-images
>>>>
>>>> (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 [hidden email]
>>>> 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 [hidden email]
>> 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/
___________________________________________________________
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/
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