Hi Yvan and list This is great news! In my limited spare time, I am currently playing with shiny as well. My current 'quick and dirty' trick goes like this: The galaxy tool creates a new shiny app and the output of the galaxy tool is a html page with the URL to the shiny app. I hope, I will have something ready to show/discuss at GCC Regards, Hans-Rudolf On 05/26/2017 04:13 PM, Yvan Le Bras wrote:

Dear Mohamed, Karim, galaxy-dev list,

A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...

Wishing you a good week end.

Cheers,

Yvan

-------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim@insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud@gmail.com> Cc : Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy

+1

On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>> wrote:

Dear all,

I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .

Thanks in Advance,

Mohamed

___________________________________________________________ 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/ <https://lists.galaxyproject.org/>

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___________________________________________________________ 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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Hi Hans, Hi everyone, I hope your return trip from GCC has been safe! Unfortunately, I didn't take time during gcc to see you Quick and dirty solution... Can we go further on this Shiny / Galaxy integration idea ? It seems that the Shiny licence can be a problem but it appears to me, if I don't make a mistake, that using the open source version of Shiny (without ssl and identification) on Galaxy through IE can be sufficent... no ? Cheers, Yvan ----- Mail d'origine ----- De: Hans-Rudolf Hotz <hrh@fmi.ch> À: Yvan Le Bras <yvan.le-bras@mnhn.fr>, Md. Rezaul Karim <rezaul.karim@insight-centre.org>, Mohamed Kassam <k.mamoud@gmail.com>, Timothée VIRGOULAY <timothee.virgoulay@mnhn.fr>, Valentin CHAMBON <valentin.chambon@mnhn.fr> Cc: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Envoyé: Mon, 29 May 2017 09:39:10 +0200 (CEST) Objet: Re: [galaxy-dev] Shiny in Galaxy Hi Yvan and list This is great news! In my limited spare time, I am currently playing with shiny as well. My current 'quick and dirty' trick goes like this: The galaxy tool creates a new shiny app and the output of the galaxy tool is a html page with the URL to the shiny app. I hope, I will have something ready to show/discuss at GCC Regards, Hans-Rudolf On 05/26/2017 04:13 PM, Yvan Le Bras wrote:

Dear Mohamed, Karim, galaxy-dev list,

A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...

Wishing you a good week end.

Cheers,

Yvan

-------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim@insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud@gmail.com> Cc : Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy

+1

On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>> wrote:

Dear all,

I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .

Thanks in Advance,

Mohamed

___________________________________________________________ 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/ <https://lists.galaxyproject.org/>

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

-- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Yvan Le Bras, PhD @Yvan2935 <°))))>< Projet 65 Millions d'observateurs Bureau 34, Station de Biologie marine BP 225, 29182 Concarneau CEDEX --- MNHN EGB/CESCO UMR 7204 43 rue Buffon 75005 PARIS tél.: +33 (0) 2 98 50 99 35 / +33 (0) 6.10.43.96.51 yvan.le-bras@mnhn.fr

Dear all I am contacting about the shiny integration into the Galaxy framewrok. Now, we are running a shiny app outside the Galaxy framework and we are pointing a link in the Galaxy tools that allow the user to open another browser for the use of the shiny app. Howerver we would like to integrate directly the shiny into Galaxy framewrok, and I would like to know if someone find a solution for doing that. Best regards Mohamed 2017-07-11 13:57 GMT+02:00 Hans-Rudolf Hotz <hrh@fmi.ch>:

Hi Yvan

Yes, after an additional week in the South of France, we traveled back safely last weekend.

I use the free version of the shiny server. In addition to what you already have mentioned, we run into another 'feature' of the free version: you cannot set the R path. You need to set the R path in the environment of the user, the shiny server is running as.

I am currently not using IE, since I cannot use Docker in our production environment. Hence the detour via an html page linking to the extra shiny server. Maybe this will change with Singularity in the future......

Using IE is definitively the way forward.

Regards, Hans-Rudolf

On 07/06/2017 10:58 PM, Yvan Le Bras wrote:

...

Hi Hans, Hi everyone,

I hope your return trip from GCC has been safe! Unfortunately, I didn't take time during gcc to see you Quick and dirty solution... Can we go further on this Shiny / Galaxy integration idea ? It seems that the Shiny licence can be a problem but it appears to me, if I don't make a mistake, that using the open source version of Shiny (without ssl and identification) on Galaxy through IE can be sufficent... no ?

Cheers,

Yvan

----- Mail d'origine ----- De: Hans-Rudolf Hotz <hrh@fmi.ch> À: Yvan Le Bras <yvan.le-bras@mnhn.fr>, Md. Rezaul Karim < rezaul.karim@insight-centre.org>, Mohamed Kassam <k.mamoud@gmail.com>, Timothée VIRGOULAY <timothee.virgoulay@mnhn.fr>, Valentin CHAMBON < valentin.chambon@mnhn.fr> Cc: Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Envoyé: Mon, 29 May 2017 09:39:10 +0200 (CEST)

Objet: Re: [galaxy-dev] Shiny in Galaxy

Hi Yvan and list

This is great news!

In my limited spare time, I am currently playing with shiny as well. My current 'quick and dirty' trick goes like this:

The galaxy tool creates a new shiny app and the output of the galaxy tool is a html page with the URL to the shiny app. I hope, I will have something ready to show/discuss at GCC

Regards, Hans-Rudolf

On 05/26/2017 04:13 PM, Yvan Le Bras wrote:

...

Dear Mohamed, Karim, galaxy-dev list,

A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...

Wishing you a good week end.

Cheers,

Yvan

-------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim@insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud@gmail.com> Cc : Galaxy Dev List <galaxy-dev@lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy

+1

On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud@gmail.com <mailto:k.mamoud@gmail.com>> wrote:

Dear all,

I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .

Thanks in Advance,

Mohamed

___________________________________________________________ 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/ <https://lists.galaxyproject.org/>

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