Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-10 Thread John Chilton 
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  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
>  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
>>>  wrote:

 Dear devs

 I've been updating the  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  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.bri...@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"
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>>
>>
>> --
>> Peter Briggs peter.bri...@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
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>   https://lists.galaxyproject.org/
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Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread 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
 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
>>  wrote:
>>>
>>> Dear devs
>>>
>>> I've been updating the  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  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.bri...@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.bri...@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:
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Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread 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
 wrote:

Dear devs

I've been updating the  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  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.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___
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  https://lists.galaxyproject.org/

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--
Peter Briggs peter.bri...@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/

Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread 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
 wrote:
> Dear devs
>
> I've been updating the  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  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.bri...@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/
___
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/

[galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread Peter Briggs 

Dear devs

I've been updating the  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  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.bri...@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/