Question: Integrate Jupyter with Galaxy
0
gravatar for niras.94
5 days ago by
niras.940
niras.940 wrote:

Hello,

I have installed a Docker Galaxy instance and i want to integrate Jupyter with it. I follow the guide in here (https://github.com/bgruening/docker-galaxy-stable), i enabled GIE and i am connecting to galaxy through my hostname not localhost or 127.0.0.1. But when i try to open rstudio, jupyter or neo (except ethercalc) they simply don't open. Have you any idea about this problem??

Thanks a lot,

Dimitris

jupyter galaxy docker • 40 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by niras.940
0
gravatar for Jennifer Hillman Jackson
5 days ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

Admin training for IEs can be found here: https://github.com/galaxyproject/dagobah-training/tree/2017-melbourne

Specifically see here for proper configuration plus an exercise: https://github.com/galaxyproject/dagobah-training/blob/2017-melbourne/sessions/21-gie/ex1-jupyter.md

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 5 days ago by Jennifer Hillman Jackson22k
0
gravatar for niras.94
5 days ago by
niras.940
niras.940 wrote:

Thanks for your help. I am running docker logs and the error that i get when i am running jupyter is this:

galaxy.web.base.interactive_environments INFO 2017-07-17 19:24:09,732 Starting docker container for IE jupyter with command [docker run -e DEBUG=false -e DEFAULT_CONTAINER_RUNTIME=120 --name=gie_2482ad8790cd4b7aa73e774cb5d2b5d5 -e "GALAXY_URL=localhost/" -e "CORS_ORIGIN=http://0.0.0.0:8080" -e "GALAXY_WEB_PORT=None" -e "HISTORY_ID=79966582feb6c081" -e "NOTEBOOK_PASSWORD=none" -e "DATASET_HID=None" -e "ADDITIONAL_IDS=None" -e "PROXY_PREFIX=" -e "API_KEY=admin" -e "REMOTE_HOST=172.17.0.1" -e "USER_EMAIL=admin@galaxy.org" -d -P -v "/export/galaxy-central/database/files/000/dataset_183.dat:/import/[183] UCSC Main on Human: knownGene (chr22:1-50818468).bed:rw" quay.io/bgruening/docker-jupyter-notebook:17.05] galaxy.web.base.interactive_environments ERROR 2017-07-17 19:24:09,806 docker: Error response from daemon: invalid bind mount spec "/export/galaxy-central/database/files/000/dataset_183.dat:/import/[183] UCSC Main on Human: knownGene (chr22:1-50818468).bed:rw": invalid volume specification: '/export/galaxy-central/database/files/000/dataset_183.dat:/import/[183] UCSC Main on Human: knownGene (chr22:1-50818468).bed:rw'. See 'docker run --help'.

galaxy.webapps.galaxy.controllers.visualization ERROR 2017-07-17 19:24:09,807 error rendering visualization (jupyter) Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/controllers/visualization.py", line 752, in render return plugin.render( trans=trans, embedded=embedded, *kwargs ) File "lib/galaxy/visualization/plugins/plugin.py", line 135, in render return self._render( render_vars, trans=trans, embedded=embedded ) File "lib/galaxy/visualization/plugins/plugin.py", line 290, in _render return trans.fill_template( template_filename, template_lookup=self.template_lookup, *render_vars ) File "lib/galaxy/web/framework/webapp.py", line 891, in fill_template return self.fill_template_mako( filename, *kwargs ) File "lib/galaxy/web/framework/webapp.py", line 905, in fill_template_mako return template.render( *data ) File "/galaxy_venv/local/lib/python2.7/site-packages/mako/template.py", line 445, in render return runtime._render(self, self.callable_, args, data) File "/galaxy_venv/local/lib/python2.7/site-packages/mako/runtime.py", line 829, in _render *_kwargs_for_callable(callable_, data)) File "/galaxy_venv/local/lib/python2.7/site-packages/mako/runtime.py", line 864, in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File "/galaxy_venv/local/lib/python2.7/site-packages/mako/runtime.py", line 890, in _exec_template callable_(context, *args, *kwargs) File "/export/galaxy-central/database/compiled_templates/jupyter.mako.py", line 79, in render_body notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/notebooks/ipython_galaxy_notebook.ipynb') File "lib/galaxy/web/base/interactive_environments.py", line 244, in url_template url = url_template.replace('${PROXY_URL}', str(self.attr.proxy_url)) \ AttributeError: 'Bunch' object has no attribute 'proxy_url' 172.17.0.1 - - [17/Jul/2017:19:24:09 +0000] "GET /plugins/interactive_environments/jupyter/show?image_tag=quay.io%2Fbgruening%2Fdocker-jupyter-notebook%3A17.05&dataset_id=9005c5112febe774&additional_dataset_ids= HTTP/1.1" 200 - "http://0.0.0.0:8080/visualization/gie_list" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/59.0.3071.115 Safari/537.36" [pid: 222|app: 0|req: 30/120] 172.17.0.1 () {44 vars in 1237 bytes} [Mon Jul 17 19:24:09 2017] GET /plugins/interactive_environments/jupyter/show?image_tag=quay.io%2Fbgruening%2Fdocker-jupyter-notebook%3A17.05&dataset_id=9005c5112febe774&additional_dataset_ids= => generated 0 bytes in 109 msecs (HTTP/1.1 200) 2 headers in 73 bytes (0 switches on core 1)

It will be very helpful if you could give a feedback about this. Thanks a lot!

ADD COMMENTlink written 5 days ago by niras.940
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