Galaxy server and ssl

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Galaxy server and ssl

Scott Szakonyi
Hello all,

Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully.

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/
Reply | Threaded
Open this post in threaded view
|

Re: Galaxy server and ssl

Dannon Baker-2
Hey Scott,

What weird behavior are you seeing?  Paste itself isn't going to serve https, though it's definitely possible to configure an upstream proxy to do so.  Are you using a setup similar to https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ?

-Dannon

On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi <[hidden email]> wrote:
Hello all,

Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully.

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/
Reply | Threaded
Open this post in threaded view
|

Re: Galaxy server and ssl

Scott Szakonyi
Hi Dannon,

There are two things I'm seeing, which seem to be independent problems.
  1. Https/ssl issue with URLs generated in util.py. It seems the detection of Https is not working properly, therefore the links underlying the toolshed functionality are coming up as http rather than https. The browser then refuses to following them because they are "mixed mode". I've gone around this for the moment by hacking the code in util.py, but it's possible (as I'm very new to server administration) that I'm missing some necessary configuration item that I just don't know about.
  2. Toolshed installation is not working properly when Galaxy is run with multiple processes. New categories are not created, and the installed tool does not show up in user menus until the Galaxy server is restarted. I've worked around this by running the Galaxy server in single process mode while installing tools.
Thanks for the link... I'll look into that and see what I can glean from it.

Best regards,

Scott

On Wed, Feb 18, 2015 at 7:14 PM, Dannon Baker <[hidden email]> wrote:
Hey Scott,

What weird behavior are you seeing?  Paste itself isn't going to serve https, though it's definitely possible to configure an upstream proxy to do so.  Are you using a setup similar to https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ?

-Dannon

On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi <[hidden email]> wrote:
Hello all,

Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully.

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/



--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/
Reply | Threaded
Open this post in threaded view
|

Re: Galaxy server and ssl

Dannon Baker-2
In reply to this post by Scott Szakonyi
You may have done this already, but if not -- can you try editing config/tool_sheds_conf.xml and change the two url entries to https?  If this file doesn't exist, create it from the .sample and then make the modifications.

-Dannon

On Thu Feb 19 2015 at 8:17:32 AM Scott Szakonyi <[hidden email]> wrote:
Hi Dannon,

There are two things I'm seeing, which seem to be independent problems.
  1. Https/ssl issue with URLs generated in util.py. It seems the detection of Https is not working properly, therefore the links underlying the toolshed functionality are coming up as http rather than https. The browser then refuses to following them because they are "mixed mode". I've gone around this for the moment by hacking the code in util.py, but it's possible (as I'm very new to server administration) that I'm missing some necessary configuration item that I just don't know about.
  2. Toolshed installation is not working properly when Galaxy is run with multiple processes. New categories are not created, and the installed tool does not show up in user menus until the Galaxy server is restarted. I've worked around this by running the Galaxy server in single process mode while installing tools.
Thanks for the link... I'll look into that and see what I can glean from it.

Best regards,

Scott

On Wed, Feb 18, 2015 at 7:14 PM, Dannon Baker <[hidden email]> wrote:
Hey Scott,

What weird behavior are you seeing?  Paste itself isn't going to serve https, though it's definitely possible to configure an upstream proxy to do so.  Are you using a setup similar to https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ?

-Dannon

On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi <[hidden email]> wrote:
Hello all,

Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully.

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/



--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/
Reply | Threaded
Open this post in threaded view
|

Re: Galaxy server and ssl

Scott Szakonyi
Hi Dannon,

Yes, that was part of what I did to make it work. I need to see if the configuration change you posted the link to earlier makes my hack unnecessary, and I'll post the results of that effort to the list.

Thanks again for your help,

Scott

On Thu, Feb 19, 2015 at 8:21 AM, Dannon Baker <[hidden email]> wrote:
You may have done this already, but if not -- can you try editing config/tool_sheds_conf.xml and change the two url entries to https?  If this file doesn't exist, create it from the .sample and then make the modifications.

-Dannon


On Thu Feb 19 2015 at 8:17:32 AM Scott Szakonyi <[hidden email]> wrote:
Hi Dannon,

There are two things I'm seeing, which seem to be independent problems.
  1. Https/ssl issue with URLs generated in util.py. It seems the detection of Https is not working properly, therefore the links underlying the toolshed functionality are coming up as http rather than https. The browser then refuses to following them because they are "mixed mode". I've gone around this for the moment by hacking the code in util.py, but it's possible (as I'm very new to server administration) that I'm missing some necessary configuration item that I just don't know about.
  2. Toolshed installation is not working properly when Galaxy is run with multiple processes. New categories are not created, and the installed tool does not show up in user menus until the Galaxy server is restarted. I've worked around this by running the Galaxy server in single process mode while installing tools.
Thanks for the link... I'll look into that and see what I can glean from it.

Best regards,

Scott

On Wed, Feb 18, 2015 at 7:14 PM, Dannon Baker <[hidden email]> wrote:
Hey Scott,

What weird behavior are you seeing?  Paste itself isn't going to serve https, though it's definitely possible to configure an upstream proxy to do so.  Are you using a setup similar to https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ?

-Dannon

On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi <[hidden email]> wrote:
Hello all,

Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully.

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/



--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.edu




--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556

http://crc.nd.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/