Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Eric Rasche]

Hi Greg,

On 11/30/2015 10:06 AM, Björn Grüning wrote:
> Hi Greg,
> 
> please have a look at:
> 
> https://github.com/bgruening/galaxytools/tree/master/visualisations
> 
> All these visualisations are self-contained. You can simply drag and
> drop them into the plugin folder and it will work. So no need for a PR.

Additionally I've opened an issue to track implementation of
visualization repos in the TS
https://github.com/galaxyproject/galaxy/issues/1191

Cheers,
Eric


> 
> I also have a hack for you to integrate this into a Docker flavour if
> you want to. Just put your Visualisation into github somewhere.
> 
> Cheers,
> Bjoern
> 
> 
>> Hello Galaxy-devs,
>>
>> I’m preparing to contribute a Visualization plug-in to the Galaxy
>> code via a PR, and I’m hoping someone can privide the details for how
>> to prepare the Javascript files that will be included in the PR.
>>
>> 1) What is the process for compressing the Javascript files?
>>
>> 2) Looking at the code base, it seems that 3rd party Javascript
>> libraries are kept in ~/static/scripts.  Should all of the 3rd party
>> libraries that are used by my plugin be added here as part of the
>> PR?
>>
>> Thanks very much,
>>
>> Greg Von Kuster
>>
>>
>> ___ 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/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:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A University
College Station, TX 77843
404-692-2048
e...@tamu.edu
___
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/mailinglists/

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Björn Grüning]

Hi Greg,

have a look here:

https://github.com/bgruening/galaxy-rna-workbench/blob/master/Dockerfile#L11


> Thanks Bjorn,
> 
> My visualization is here:
> https://github.com/gregvonkuster/galaxy-csg/tree/master/visualizations/csg,
> so can you provide your docker hack?
> 
> In addition to including this into docker, I would like it to be
> available to Galaxy instances outside of docker.  What is the general
> process for doing this?  How does a Galaxy admin find out that this
> particular visualization exists and where to get it?

In the long run I would like to have the ToolShed providing
visualisations. For the time being the best thing we can do is to join
github repositories to have as less as possible. So the few repos out
there get more attraction.

Cheers,
Bjoern

> Thanks!
> 
> Greg Von Kuster
> 
> 
>> On Nov 30, 2015, at 11:06 AM, Björn Grüning
>>  wrote:
>> 
>> Hi Greg,
>> 
>> please have a look at:
>> 
>> https://github.com/bgruening/galaxytools/tree/master/visualisations
>>
>>
>> 
All these visualisations are self-contained. You can simply drag and
>> drop them into the plugin folder and it will work. So no need for a
>> PR.
>> 
>> I also have a hack for you to integrate this into a Docker flavour
>> if you want to. Just put your Visualisation into github somewhere.
>> 
>> Cheers, Bjoern
>> 
>> 
>>> Hello Galaxy-devs,
>>> 
>>> I’m preparing to contribute a Visualization plug-in to the
>>> Galaxy code via a PR, and I’m hoping someone can privide the
>>> details for how to prepare the Javascript files that will be
>>> included in the PR.
>>> 
>>> 1) What is the process for compressing the Javascript files?
>>> 
>>> 2) Looking at the code base, it seems that 3rd party Javascript 
>>> libraries are kept in ~/static/scripts.  Should all of the 3rd
>>> party libraries that are used by my plugin be added here as part
>>> of the PR?
>>> 
>>> Thanks very much,
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> ___
>>> 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/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:
  https://lists.galaxyproject.org/

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

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Greg Von Kuster]

Thanks Bjorn,

My visualization is here: 
https://github.com/gregvonkuster/galaxy-csg/tree/master/visualizations/csg, so 
can you provide your docker hack?  

In addition to including this into docker, I would like it to be available to 
Galaxy instances outside of docker.  What is the general process for doing 
this?  How does a Galaxy admin find out that this particular visualization 
exists and where to get it?

Thanks!

Greg Von Kuster


> On Nov 30, 2015, at 11:06 AM, Björn Grüning  wrote:
> 
> Hi Greg,
> 
> please have a look at:
> 
> https://github.com/bgruening/galaxytools/tree/master/visualisations
> 
> All these visualisations are self-contained. You can simply drag and
> drop them into the plugin folder and it will work. So no need for a PR.
> 
> I also have a hack for you to integrate this into a Docker flavour if
> you want to. Just put your Visualisation into github somewhere.
> 
> Cheers,
> Bjoern
> 
> 
>> Hello Galaxy-devs,
>> 
>> I’m preparing to contribute a Visualization plug-in to the Galaxy
>> code via a PR, and I’m hoping someone can privide the details for how
>> to prepare the Javascript files that will be included in the PR.
>> 
>> 1) What is the process for compressing the Javascript files?
>> 
>> 2) Looking at the code base, it seems that 3rd party Javascript
>> libraries are kept in ~/static/scripts.  Should all of the 3rd party
>> libraries that are used by my plugin be added here as part of the
>> PR?
>> 
>> Thanks very much,
>> 
>> Greg Von Kuster
>> 
>> 
>> ___ 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/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:
  https://lists.galaxyproject.org/

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

[galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Greg Von Kuster]

Hello Galaxy-devs,

I’m preparing to contribute a Visualization plug-in to the Galaxy code via a 
PR, and I’m hoping someone can privide the details for how to prepare the 
Javascript files that will be included in the PR.  

1) What is the process for compressing the Javascript files?

2) Looking at the code base, it seems that 3rd party Javascript libraries are 
kept in ~/static/scripts.  Should all of the 3rd party libraries that are used 
by my plugin be added here as part of the PR?

Thanks very much,

Greg Von Kuster


___
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/mailinglists/

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Björn Grüning]

Hi Greg,

please have a look at:

https://github.com/bgruening/galaxytools/tree/master/visualisations

All these visualisations are self-contained. You can simply drag and
drop them into the plugin folder and it will work. So no need for a PR.

I also have a hack for you to integrate this into a Docker flavour if
you want to. Just put your Visualisation into github somewhere.

Cheers,
Bjoern


> Hello Galaxy-devs,
> 
> I’m preparing to contribute a Visualization plug-in to the Galaxy
> code via a PR, and I’m hoping someone can privide the details for how
> to prepare the Javascript files that will be included in the PR.
> 
> 1) What is the process for compressing the Javascript files?
> 
> 2) Looking at the code base, it seems that 3rd party Javascript
> libraries are kept in ~/static/scripts.  Should all of the 3rd party
> libraries that are used by my plugin be added here as part of the
> PR?
> 
> Thanks very much,
> 
> Greg Von Kuster
> 
> 
> ___ 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/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:
  https://lists.galaxyproject.org/

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

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Greg Von Kuster]

Thanks for the hint on how to make this available in the Docker flavor Bjorn!  
;)

> On Nov 30, 2015, at 12:14 PM, Björn Grüning  wrote:
> 
> 
> Hi Greg,
> 
> have a look here:
> 
> https://github.com/bgruening/galaxy-rna-workbench/blob/master/Dockerfile#L11
> 
> 
>> Thanks Bjorn,
>> 
>> My visualization is here:
>> https://github.com/gregvonkuster/galaxy-csg/tree/master/visualizations/csg,
>> so can you provide your docker hack?
>> 
>> In addition to including this into docker, I would like it to be
>> available to Galaxy instances outside of docker.  What is the general
>> process for doing this?  How does a Galaxy admin find out that this
>> particular visualization exists and where to get it?
> 
> In the long run I would like to have the ToolShed providing
> visualisations. For the time being the best thing we can do is to join
> github repositories to have as less as possible. So the few repos out
> there get more attraction.
> 
> Cheers,
> Bjoern
> 
>> Thanks!
>> 
>> Greg Von Kuster
>> 
>> 
>>> On Nov 30, 2015, at 11:06 AM, Björn Grüning
>>>  wrote:
>>> 
>>> Hi Greg,
>>> 
>>> please have a look at:
>>> 
>>> https://github.com/bgruening/galaxytools/tree/master/visualisations
>>> 
>>> 
>>> 
> All these visualisations are self-contained. You can simply drag and
>>> drop them into the plugin folder and it will work. So no need for a
>>> PR.
>>> 
>>> I also have a hack for you to integrate this into a Docker flavour
>>> if you want to. Just put your Visualisation into github somewhere.
>>> 
>>> Cheers, Bjoern
>>> 
>>> 
 Hello Galaxy-devs,
 
 I’m preparing to contribute a Visualization plug-in to the
 Galaxy code via a PR, and I’m hoping someone can privide the
 details for how to prepare the Javascript files that will be
 included in the PR.
 
 1) What is the process for compressing the Javascript files?
 
 2) Looking at the code base, it seems that 3rd party Javascript 
 libraries are kept in ~/static/scripts.  Should all of the 3rd
 party libraries that are used by my plugin be added here as part
 of the PR?
 
 Thanks very much,
 
 Greg Von Kuster
 
 
 ___
 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/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:
  https://lists.galaxyproject.org/

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

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

[Greg Von Kuster]

Thanks Eric,

It seems to be the case currently that there is no way to easily share 
visualization plugins outside of using Docker, which is unfortunate.  As an 
interim solution, would it work to allow visualization code to be added to the 
Galaxy code base via PRs?  Otherwise, those that are not using Docker Galaxy 
flavors likey willl not locate the plugins that are necessary for the tools 
that can currently be installed from the Tool Shed.  

For example, all of these tools which are currently available in the Test Tool 
Shed and soon will be available in the Main Tool Shed require a plugin:

https://testtoolshed.g2.bx.psu.edu/view/greg/icqsol_add_surface_field_from_expression/f239d7513008
https://testtoolshed.g2.bx.psu.edu/view/greg/icqsol_color_surface_field/6a5b5cc5b885
https://testtoolshed.g2.bx.psu.edu/view/greg/icqsol_compose_shapes/36f5fa5bd6d9
https://testtoolshed.g2.bx.psu.edu/view/greg/icqsol_create_shape/d1d206669437
https://testtoolshed.g2.bx.psu.edu/view/greg/icqsol_refine_shape/a38daf377d55

Thanks again,

Greg

> On Nov 30, 2015, at 12:24 PM, Eric Rasche  wrote:
> 
> Hi Greg,
> 
> On 11/30/2015 10:06 AM, Björn Grüning wrote:
>> Hi Greg,
>> 
>> please have a look at:
>> 
>> https://github.com/bgruening/galaxytools/tree/master/visualisations
>> 
>> All these visualisations are self-contained. You can simply drag and
>> drop them into the plugin folder and it will work. So no need for a PR.
> 
> Additionally I've opened an issue to track implementation of
> visualization repos in the TS
> https://github.com/galaxyproject/galaxy/issues/1191
> 
> Cheers,
> Eric
> 
> 
>> 
>> I also have a hack for you to integrate this into a Docker flavour if
>> you want to. Just put your Visualisation into github somewhere.
>> 
>> Cheers,
>> Bjoern
>> 
>> 
>>> Hello Galaxy-devs,
>>> 
>>> I’m preparing to contribute a Visualization plug-in to the Galaxy
>>> code via a PR, and I’m hoping someone can privide the details for how
>>> to prepare the Javascript files that will be included in the PR.
>>> 
>>> 1) What is the process for compressing the Javascript files?
>>> 
>>> 2) Looking at the code base, it seems that 3rd party Javascript
>>> libraries are kept in ~/static/scripts.  Should all of the 3rd party
>>> libraries that are used by my plugin be added here as part of the
>>> PR?
>>> 
>>> Thanks very much,
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> ___ 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/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:
>>  https://lists.galaxyproject.org/
>> 
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>> 
> 
> -- 
> Eric Rasche
> Programmer II
> 
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
> ___
> 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/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:
  https://lists.galaxyproject.org/

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

Re: [galaxy-dev] Error installing tools from toolshed

[Scott Szakonyi]

Nicola,

Sorry for the delay... holidays here in the US. That worked perfectly...
thank you very much!

Best,

Scott

On Fri, Nov 20, 2015 at 1:59 PM, Nicola Soranzo  wrote:

> Hi Scott,
> you can try to reinstall it with: "Admin" -> "Manage installed tools",
> then click on "Advanced Search" on top, then click on "Deactivated or
> uninstalled" and click on "Activate or reinstall" on Trimmomatic menu.
>
> Cheers,
> Nicola
>
>
> On 20/11/15 18:07, Scott Szakonyi wrote:
>
> Hi Nicola,
>
> Certainly. On screen, I get a message that says "Revision *f8a9a5eaca8a* of
> repository *trimmomatic* owned by *pjbriggs* has already been installed."
>
> In the logs:
>
> 129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET
> /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/install_latest_repository_revision?id=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.
> HTTP/1.1" 200 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
> 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET
> /admin_toolshed/browse_repositories?operation=install+latest+revision=d071e794759ab192
> HTTP/1.1" 302 - "
> https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.;
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML,
> like Gecko) Chrome/46.0.2490.80 Safari/537.36"
>
> I'm not 100% sure these are in order... I have multiple web handlers
> running and the requests get spread out between them. I've tried to order
> them as best I can.
>
> Thanks!
>
> Scott
>
> On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo 
> wrote:
>
>> Hi Scott,
>> can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage
>> installed tools" and click on "Install latest revision" on Trimmomatic
>> menu) ?
>> If this does not work, copy the relevant log from the Galaxy server and
>> post it on the mailing list.
>>
>> Cheers,
>> Nicola
>>
>>
>> On 20/11/15 17:23, Scott Szakonyi wrote:
>>
>> I was able to switch over to GitHub without issue. Thanks for pointing me
>> in the right direction.
>>
>> I have installed Trimmomatic successfully, although I wasn't able to
>> install the latest version. If I try to install the "2015-09-23" revision,
>> I get "Internal Server Error Galaxy was unable to successfully complete
>> your request". The "2015-04-22" revision installs without issue.
>>
>> I'm still having troubles with Picard as well, but one thing at a time!
>> What information can I provide that might help with getting the latest
>> issue of Trimmomatic?
>>
>> Thanks!
>>
>> On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo < 
>> nsora...@tiscali.it> wrote:
>>
>>> Hi Scott,
>>> the mercurial mirror is not up to date unfortunately, see this previous
>>> discussion:
>>>
>>>
>>> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html
>>>
>>> Cheers,
>>> Nicola
>>>
>>>
>>> On 20/11/15 13:13, Scott Szakonyi wrote:
>>>
>>> Hi Nicola,
>>>
>>> I'm not entirely sure which version... but I am still using the
>>> mercurial mirror, which says I'm up to date. Would this be a wise time,
>>> then, to change over to the Git repository directly?
>>>
>>> Thanks!
>>>
>>> Scott
>>>
>>> On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo < 
>>> nsora...@tiscali.it> wrote:
>>>
 Hi Scott,
 which Galaxy release are you using?
 This is a bug which should be fixed in an updated release_15.07 git
 branch.

 Cheers,
 Nicola

  Scott Szakonyi