removing wrapper version info from tools?

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removing wrapper version info from tools?

Nikhil Joshi-2
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.

--
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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Re: removing wrapper version info from tools?

Björn Grüning-3
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.
>
>
>
> ___________________________________________________________
> 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/
>
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in your mail client.  To manage your subscriptions to this
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Re: removing wrapper version info from tools?

Björn Grüning-3
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 <[hidden email]>
> 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.
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>>
>
>
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in your mail client.  To manage your subscriptions to this
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Re: removing wrapper version info from tools?

Nikhil Joshi-2
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 <[hidden email]> 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 <[hidden email]>
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.



___________________________________________________________
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/







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

___________________________________________________________
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/

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  http://galaxyproject.org/search/mailinglists/
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Re: removing wrapper version info from tools?

Björn Grüning-3
Hi Nik,

sorry for my late response.

Am 09.07.2014 01:23, schrieb Nikhil Joshi:

> 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.

Please remember you are then forced to maintain the tools all by your
own and integrate changes from upstream by your own. I'm not sure that
is worth the effort.

> What would be the best way
> to have multiple versions of a tool *without* using the toolshed? Any help
> is highly appreciated. Thanks!

I don't think that is possible at all. In the end that is one reason the
Tool Shed project was started. To make it possible to have many
different tool versions and to spread the maintenance burden over the
entire community.
Have a look at the galaxytools repository, maintained by several people:
https://github.com/bgruening/galaxytools

We accept PR and you are very welcome to work with us to improve the
tools, in the end I really think it will save you some time.

An other really easy possibility is ... just remove the tool-version
from the HTML rendering. If you are not afraid of maintaining in house
patches, that should be fine and will take time, I guess.

Cheers,
Bjoern

> - Nik.
>
>
> On Tue, Jul 8, 2014 at 1:12 AM, Björn Grüning <[hidden email]>
> 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 <[hidden email]
>>>>
>>> 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.
>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> 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/
>>>>>
>>>>>
>>>>>
>>>
>>>
>
>
___________________________________________________________
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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