Hi Bjorn,

So I actually don't use the toolshed at all, we have a galaxy AMI that I
update and maintain. We have many of the canonical tools, but we also have
many custom tool interfaces on there, some of which I wrote. We also use
the latest version of the tool if possible. All of the XML files are local
to the instance and are not from the toolshed. I am referring to the
version that is used in the "<tool>" tag. That version number seems
arbitrary and the students that use our Galaxy are constantly confused as
to why the tool page has a different version than the tool itself. However,
it seems like there is no easy way to remove that part, so I think I will
just have to update the version numbers myself. What would be the best way
to have multiple versions of a tool *without* using the toolshed? Any help
is highly appreciated. Thanks!

- Nik.


On Tue, Jul 8, 2014 at 1:12 AM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> Hi Nik,
>
>  Hi Bjorn,
>>
>> Thanks for your response. It seems to me that the wrapper version is not
>> really that useful... the thing that is important is the version of the
>> underlying tool.
>>
>
> Sure, I agree. But on the other side the user should not care about the
> version, and is on most cases not interested as long as it works :)
> But as pointed out I would also like to shift to a more useful numbering,
> that the arbitrary one we are using now.
>
>
> I can certainly update the versions to be the versions of
>
>> the tool, if need be.
>>
>
> That will break many thing, if you combining your tools with the toolshed
> and updates would be more complicated. Don't do that, at least not for
> tools from the ToolShed. Try to convince the Tool Maintainers.
>
>
> However, I wasn't aware that you could have multiple
>
>> versions of the same tool to choose from. How do I get that to work?
>>
>
> You can simply install multiple versions (revisions) from the same tool
> from the Tool Shed. For example multimple Blast version.
>
>
>  I tried creating two different XML files with the same tool id, but that
>> didn't work. And how would I make sure the wrapper scripts pointed to the
>> correct version... it seems like I would have to tailor each script with
>> an
>> absolute path to the specific version....?
>>
>
> No you need to have the Tool Shed managing that for you. Each version is a
> separate tool with the same tool-id. Galaxy keeps track of every dependency
> of a certain tool. So the same tool with different versions with different
> dependencies will be working over time.
>
> Please read more about all of that in the galaxy wiki, especially about
> Tools and the Tool Shed:
>
> https://wiki.galaxyproject.org/ToolShed
>
> Cheers,
> Bjoern
>
>
>  - Nik.
>>
>>
>> On Mon, Jul 7, 2014 at 11:56 PM, Björn Grüning <bjoern.gruen...@gmail.com
>> >
>> wrote:
>>
>>  Hi Nik,
>>>
>>> you can hack to tool rendering and omit the version string, but I would
>>> not recommend that. The version will be a selectbox as soon as you have
>>> multiple versions from the same tools installed. This is important for
>>> reproducibility.
>>> The best approach would be to fix the version string. Do you have any
>>> suggestions?
>>> For my wrappers I try to go with that version scheme:
>>> {Tool-Version}.{wrapper-version}.
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> Am 08.07.2014 08:51, schrieb Nikhil Joshi:
>>>
>>>  Hi all,
>>>>
>>>> So I am trying to remove the version info (at the top of a tool page)
>>>> entirely for all the tools. As I understand, those versions are the
>>>> versions of the wrappers and not the tools themselves. Although I could
>>>> change that, I would rather just not have the versions on the tool pages
>>>> at
>>>> all. We currently show all the versions of our tools on our landing
>>>> page.
>>>> Is there any way to remove the version part of the tool title entirely?
>>>> I.e., if it originally says "Map with BWA for Illumina (version
>>>> 1.0.0)", I
>>>> just want it to say "Map with BWA for Illumina".
>>>>
>>>> - Nik.
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
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>>>>
>>>>
>>>>
>>
>>


-- 
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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