[galaxy-dev] jupyter notebook / nginx / ssl
Hi Galaxy developers, we are trying to get notebooks to run on our production server, with half success: we can get jupyter to load, and it does access the history, but notebooks uploaded to history do not load, and any modification to the notebook provided can be saved but do not show up when the notebook is re-opened. we're running NGINX and have SSL certs in place. Any idea how to fix this? Thanks Cris ___ 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/
[galaxy-dev] jupyter + apache proxy + SSL
Hi,
I am trying to set up galaxy server with IE jupyter with apache proxy and SSL
enbled.
Does anybody have a similar setup? I am using
== galaxy.ini
dynamic_proxy_manage=False ('True' gives the same error)
dynamic_proxy=node
dynamic_proxy_session_map=database/session_map.sqlite
#dynamic_proxy_bind_port=8800
#dynamic_proxy_bind_ip=0.0.0.0
dynamic_proxy_external_proxy=True
dynamic_proxy_prefix=gie_proxy
== httpd.conf
ProxyPass/gie_proxy/jupyter/ipython/api/kernels
ws://localhost:8800/gie_proxy/jupyter/ipython/api/kernels
VirtualHost _default_:80>
RewriteEngine on
ReWriteCond %{SERVER_PORT} !^443$
RewriteRule ^/(.*) https://%{HTTP_HOST}/$1 [NC,R,L]
It works fine with HTTP but not HTTPS and, naturally, I get
jquery.js:10261 Mixed Content: The page at 'https://mydomain.xx/' was loaded
over HTTPS, but requested an insecure XMLHttpRequest endpoint
'http://mydomain.xx/gie_proxy/jupyter/ipython/login?next=%2Fgie_proxy%2Fjupyter%2Fipython%2Ftree'.
This request has been blocked; the content must be served over HTTPS.
Is there a way to modify the container config such that it runs on a https, or
is there a galaxy configuration routine I can use?
Thank you
Nikolay
===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
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Re: [galaxy-dev] Jupyter
If fixed this in the container, builds are triggered, so hopefully in a few hour you can pull the new image and this is working for you! Thanks for reporting! Bjoern > Thanks, almost worked… > > get --id 78 > bash: /home/jovyan/py/get: Permission denied > > I assume the jovyan is a docker user? > > > > > > On 10/02/16 15:36, "Björn Grüning" wrote: > >> >> >> Am 10.02.2016 um 15:25 schrieb Jasper Koehorst: >>> I am currently experimenting with jupyter and it finally works as I am >>> able to use the environment on a local machine. >>> However beside python2.7 how do I load a galaxy history file into for >>> example R, Bash, etc? I could not really find any documentation on these >>> languages beside python 2.7. >>> Is there a website for best practices? >> >> You should have a `get` and a `put` commandline tools in your PATH. >> >> So from bash you should be able to do `get --id 1`. >> >> https://github.com/bgruening/docker-jupyter-notebook/blob/master/get >> >> Hope this works, >> Bjoern >> >> >>> Kind regards, >>> >>> Jasper >>> >>> >>> >>> ___ >>> 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] Jupyter
Thanks, almost worked… get --id 78 bash: /home/jovyan/py/get: Permission denied I assume the jovyan is a docker user? On 10/02/16 15:36, "Björn Grüning" wrote: > > >Am 10.02.2016 um 15:25 schrieb Jasper Koehorst: >> I am currently experimenting with jupyter and it finally works as I am >> able to use the environment on a local machine. >> However beside python2.7 how do I load a galaxy history file into for >> example R, Bash, etc? I could not really find any documentation on these >> languages beside python 2.7. >> Is there a website for best practices? > >You should have a `get` and a `put` commandline tools in your PATH. > >So from bash you should be able to do `get --id 1`. > >https://github.com/bgruening/docker-jupyter-notebook/blob/master/get > >Hope this works, >Bjoern > > >> Kind regards, >> >> Jasper >> >> >> >> ___ >> 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] Jupyter
Am 10.02.2016 um 15:25 schrieb Jasper Koehorst: > I am currently experimenting with jupyter and it finally works as I am > able to use the environment on a local machine. > However beside python2.7 how do I load a galaxy history file into for > example R, Bash, etc? I could not really find any documentation on these > languages beside python 2.7. > Is there a website for best practices? You should have a `get` and a `put` commandline tools in your PATH. So from bash you should be able to do `get --id 1`. https://github.com/bgruening/docker-jupyter-notebook/blob/master/get Hope this works, Bjoern > Kind regards, > > Jasper > > > > ___ > 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] Jupyter
I am currently experimenting with jupyter and it finally works as I am able to use the environment on a local machine. However beside python2.7 how do I load a galaxy history file into for example R, Bash, etc? I could not really find any documentation on these languages beside python 2.7. Is there a website for best practices? Kind regards, Jasper ___ 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/
