Refactor to just be jupyter-desktop (#1)
Refactor to just be jupyter-desktop
This commit is contained in:
Yuvi Panda
GitHub
commit
e39bd9a1b1
87
Dockerfile
87
Dockerfile
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FROM jupyter/base-notebook:1386e2046833
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USER root
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# Useful tools for debugging connection problems
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RUN apt-get update -y -q && \
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apt-get install -y -q \
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curl \
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net-tools \
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vim
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# Desktop environment, keep in sync with jupyter_notebook_config.py
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# ENV DESKTOP_PACKAGE lxde
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ENV DESKTOP_PACKAGE xfce4
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RUN apt-get update -y -q && \
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apt-get install -y -q \
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xterm \
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${DESKTOP_PACKAGE}
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# Don't install distro versions of tigervnc and websockify, instead install
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# upstream versions
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# Novnc: just want web files
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RUN cd /opt && \
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curl -sSfL https://github.com/novnc/noVNC/archive/v1.1.0.tar.gz | tar -zxf -
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# Patch novnc to use correct path to websockify (defaults to /)
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# Note if you use vnc.html you will need to patch ui.js to use the correct path
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# and also to override localstorage which may store an incorrect path from a
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# different session
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# Also resize server instead of scaling client
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RUN sed -i.bak \
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-e "s%\('path', 'websockify'\)%'path', window.location.pathname.replace(/[^/]*$/, '').substring(1) + 'websockify'); console.log('websockify path:' + path%" \
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-re "s%rfb.scaleViewport = .+%rfb.resizeSession = readQueryVariable('resize', true);%" \
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/opt/noVNC-1.1.0/vnc_lite.html
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# Install tigervnc to /usr/local
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RUN curl -sSfL 'https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.9.0.x86_64.tar.gz' | tar -zxf - -C /usr/local --strip=2
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USER jovyan
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# Custom jupyter-server-proxy to load vnc_lite.html instead of /
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# https://github.com/jupyterhub/jupyter-server-proxy/pull/151
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RUN /opt/conda/bin/pip install https://github.com/manics/jupyter-server-proxy/archive/1f22ccf44abd7ab5f7b306d57b6adb1dc3190e8b.zip
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RUN conda install -y -q -c manics websockify=0.9.0
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ADD jupyter_notebook_config.py /home/jovyan/.jupyter/jupyter_notebook_config.py
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########## Applications
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USER root
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RUN apt-get update -y -q && \
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apt-get install -y -q \
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firefox \
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less \
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openjdk-8-jre \
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unzip
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# default-jre is java 11 which is incompatible with Fiji
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USER jovyan
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RUN wget -q https://downloads.imagej.net/fiji/latest/fiji-nojre.zip && \
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unzip -q fiji-nojre.zip && \
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echo TODO: rm fiji-nojre.zip
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RUN wget -q https://github.com/ome/omero-insight/releases/download/v5.5.6/OMERO.imagej-5.5.6.zip && \
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cd Fiji.app/plugins && \
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unzip -q ../../OMERO.imagej-5.5.6.zip && \
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echo TODO: rm OMERO.imagej-5.5.6.zip
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RUN wget -q https://github.com/ome/omero-insight/releases/download/v5.5.6/OMERO.insight-5.5.6.zip && \
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unzip -q OMERO.insight-5.5.6.zip && \
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echo TODO: rm OMERO.insight-5.5.6.zip
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RUN mkdir .java && \
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cd OMERO.insight-5.5.6 && \
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wget -q https://www.openmicroscopy.org/img/logos/omero-logomark.svg
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# https://developer.gnome.org/desktop-entry-spec/
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#COPY --chown=${NB_UID}:${NB_GID} *.desktop /home/jovyan/Desktop/
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COPY --chown=1000:100 *.desktop /home/jovyan/Desktop/
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# Configure default OMERO.insight server list
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#COPY --chown=${NB_UID}:${NB_GID} java_userPrefs .java/.userPrefs
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COPY --chown=1000:100 java_userPrefs .java/.userPrefs
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WORKDIR ${HOME}
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# Both these should work:
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# http://127.0.0.1:8888/desktop
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# http://localhost:5901/vnc.html
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14
Fiji.desktop
14
Fiji.desktop
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[Desktop Entry]
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Version=1.0
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Name=Fiji Is Just ImageJ
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GenericName=Fiji Is Just ImageJ
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X-GNOME-FullName=Fiji Is Just ImageJ
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Comment=Scientific Image Analysis
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Type=Application
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Categories=Education;Science;ImageProcessing;
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Exec=/home/jovyan/Fiji.app/ImageJ-linux64
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TryExec=/home/jovyan/Fiji.app/ImageJ-linux64
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Terminal=false
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StartupNotify=true
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Icon=/home/jovyan/Fiji.app/images/icon.png
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StartupWMClass=fiji-Main
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[Desktop Entry]
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Version=1.0
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Name=OMERO.insight
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GenericName=OMERO.insight
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X-GNOME-FullName=OMERO.insight
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Comment=OMERO desktop client
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Type=Application
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Categories=Education;Science;ImageProcessing;
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Exec=/home/jovyan/OMERO.insight-5.5.6/bin/omero-insight
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TryExec=/home/jovyan/OMERO.insight-5.5.6/bin/omero-insight
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Terminal=false
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StartupNotify=true
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Icon=/home/jovyan/OMERO.insight-5.5.6/omero-logomark.svg
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15
README.md
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README.md
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# Jupyter OMERO client Desktop
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[](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/master?urlpath=Desktop)
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# Jupyter OMERO/Fiji/Napari Desktop
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[](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/napari-binder?filepath=napari.ipynb)
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Run OMERO clients in a Linux desktop using Jupyter.
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Run [OMERO clients](https://www.openmicroscopy.org/omero/downloads/) and [Napari](http://napari.org/) in a Linux desktop using Jupyter.
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This is based on https://github.com/ryanlovett/nbnovnc
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Either [run on mybinder.org](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/napari-binder?filepath=napari.ipynb) or build locally with [repo2docker](https://repo2docker.readthedocs.io/):
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```
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docker build -t jupyter-omeroanalysis-desktop .
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docker run -it --rm -p 8888:8888 jupyter-omeroanalysis-desktop
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repo2docker .
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```
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Open the displayed URL, then go to `/Desktop` e.g. http://localhost:8888/Desktop and if you're lucky you'll see a Linux desktop with icons for OMERO.insight and FIJI.
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Open the displayed URL, then go to `/desktop` e.g. http://localhost:8888/desktop and if you're lucky you'll see a Linux desktop with icons for OMERO.insight and FIJI.
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Once the desktop is open go back to the main Jupyter Notebook window, open `napari.ipynb` and execute the cells one at a time. You should see Napari open in the desktop window.
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dbus-x11
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firefox
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xfce4
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xfce4-panel
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xfce4-session
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xfce4-settings
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xorg
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xubuntu-icon-theme
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channels:
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- manics
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dependencies:
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- websockify
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- pip:
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- https://github.com/jupyterhub/jupyter-server-proxy/archive/0e67e1afd0bab1342443f13bd147a2f8c682e9e0.zip
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0">
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<entry key="omeroConnectionSpeed" value="0"/>
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<entry key="omeroServer" value="nightshade.openmicroscopy.org:4064,outreach.openmicroscopy.org:4064,idr.openmicroscopy.org:4064,demo.openmicroscopy.org:4064"/>
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<entry key="omeroTransferEncrypted" value="true"/>
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</map>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0"/>
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
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<map MAP_XML_VERSION="1.0"/>
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import os
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def setup_desktop():
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VNC_APPLICATION_DIR = os.path.join(os.getenv('CONDA_DIR'), 'vnc')
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return {
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'command': [
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'websockify', '-v',
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'--web', VNC_APPLICATION_DIR + '/noVNC-1.1.0',
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'--heartbeat', '30',
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'5901',
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'--unix-target', VNC_APPLICATION_DIR + '/socket',
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'--',
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VNC_APPLICATION_DIR + '/bin/vncserver',
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'-verbose',
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'-xstartup', VNC_APPLICATION_DIR + '/xstartup',
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'-geometry', '1024x768',
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'-SecurityTypes', 'None',
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'-rfbunixpath', VNC_APPLICATION_DIR + '/socket',
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'-fg',
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':1',
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],
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'port': 5901,
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'timeout': 30,
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'mappath': {'/': '/vnc_lite.html'},
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}
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import os
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if os.getenv('DESKTOP_PACKAGE') == 'lxde':
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xstartup = 'startlxde'
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elif os.getenv('DESKTOP_PACKAGE') == 'xfce4':
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xstartup = 'xfce4-session'
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else:
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xstartup = 'xterm'
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vnc_socket = os.path.join(os.getenv('HOME'), '.vnc', 'socket')
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c.ServerProxy.servers = {
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'Desktop': {
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'command': [
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'/opt/conda/bin/websockify',
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'-v',
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'--web', '/opt/noVNC-1.1.0',
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'--heartbeat', '30',
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'5901',
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'--unix-target', vnc_socket,
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'--',
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'vncserver',
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'-verbose',
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'-xstartup', xstartup,
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'-geometry', '1024x768',
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'-SecurityTypes', 'None',
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'-rfbunixpath', vnc_socket,
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'-fg',
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':1',
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],
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'absolute_url': False,
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'port': 5901,
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'timeout': 30,
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'mappath': {'/': '/vnc_lite.html'},
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}
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}
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#!/bin/bash
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set -eux
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env
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VNC_APPLICATION_DIR=$CONDA_DIR/vnc
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mkdir $VNC_APPLICATION_DIR
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pushd $VNC_APPLICATION_DIR
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# Novnc: just want web files
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curl -sSfL https://github.com/novnc/noVNC/archive/v1.1.0.tar.gz | tar -zxf -
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# Install tigervnc
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curl -sSfL 'https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.9.0.x86_64.tar.gz' | tar -zxf - --strip=2
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# Patch novnc to use correct path to websockify (defaults to /)
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# Note if you use vnc.html you will need to patch ui.js to use the correct path
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# and also to override localstorage which may store an incorrect path from a
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# different session
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# Also resize server instead of scaling client
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sed -i.bak \
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-e "s%\('path', 'websockify'\)%'path', window.location.pathname.replace(/[^/]*$/, '').substring(1) + 'websockify'); console.log('websockify path:' + path%" \
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-re "s%rfb.scaleViewport = .+%rfb.resizeSession = readQueryVariable('resize', true);%" \
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noVNC-1.1.0/vnc_lite.html
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cp $REPO_DIR/share/xstartup .
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chmod +x xstartup
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pip install $REPO_DIR
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import setuptools
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setuptools.setup(
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name="jupyter-desktop-server",
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# py_modules rather than packages, since we only have 1 file
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py_modules=['jupyter_desktop'],
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entry_points={
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'jupyter_serverproxy_servers': [
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'desktop = jupyter_desktop:setup_desktop',
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]
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},
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install_requires=['jupyter-server-proxy'],
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package_data={
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'jupyter_desktop': ['desktop/*'],
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},
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)
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#!/bin/sh
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exec /usr/bin/dbus-launch xfce4-session
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