Browse Source

Jupyter Linux Desktop with OMERO clients

tags/v0.1
Simon Li 7 months ago
parent
commit
051389e401
12 changed files with 125 additions and 9 deletions
  1. +39
    -2
      Dockerfile
  2. +14
    -0
      Fiji.desktop
  3. +29
    -0
      LICENSE
  4. +13
    -0
      OMERO.insight.desktop
  5. +7
    -6
      README.md
  6. +3
    -0
      java_userPrefs/org/openmicroscopy/prefs.xml
  7. +3
    -0
      java_userPrefs/org/openmicroscopy/shoola/prefs.xml
  8. +3
    -0
      java_userPrefs/org/openmicroscopy/shoola/util/prefs.xml
  9. +7
    -0
      java_userPrefs/org/openmicroscopy/shoola/util/ui/login/prefs.xml
  10. +3
    -0
      java_userPrefs/org/openmicroscopy/shoola/util/ui/prefs.xml
  11. +3
    -0
      java_userPrefs/org/prefs.xml
  12. +1
    -1
      jupyter_notebook_config.py

+ 39
- 2
Dockerfile View File

@@ -1,4 +1,4 @@
FROM jupyter/base-notebook
FROM jupyter/base-notebook:1386e2046833

USER root
# Useful tools for debugging connection problems
@@ -11,7 +11,8 @@ RUN apt-get update -y -q && \
# Desktop environment, keep in sync with jupyter_notebook_config.py
# ENV DESKTOP_PACKAGE lxde
ENV DESKTOP_PACKAGE xfce4
RUN apt-get install -y -q \
RUN apt-get update -y -q && \
apt-get install -y -q \
xterm \
${DESKTOP_PACKAGE}

@@ -41,8 +42,44 @@ USER jovyan
# https://github.com/jupyterhub/jupyter-server-proxy/pull/151
RUN /opt/conda/bin/pip install https://github.com/manics/jupyter-server-proxy/archive/1f22ccf44abd7ab5f7b306d57b6adb1dc3190e8b.zip
RUN conda install -y -q -c manics websockify=0.9.0

ADD jupyter_notebook_config.py /home/jovyan/.jupyter/jupyter_notebook_config.py


########## Applications

USER root
RUN apt-get update -y -q && \
apt-get install -y -q \
firefox \
less \
openjdk-8-jre \
unzip
# default-jre is java 11 which is incompatible with Fiji

USER jovyan
RUN wget -q https://downloads.imagej.net/fiji/latest/fiji-nojre.zip && \
unzip -q fiji-nojre.zip && \
echo TODO: rm fiji-nojre.zip
RUN wget -q https://github.com/ome/omero-insight/releases/download/v5.5.6/OMERO.imagej-5.5.6.zip && \
cd Fiji.app/plugins && \
unzip -q ../../OMERO.imagej-5.5.6.zip && \
echo TODO: rm OMERO.imagej-5.5.6.zip

RUN wget -q https://github.com/ome/omero-insight/releases/download/v5.5.6/OMERO.insight-5.5.6.zip && \
unzip -q OMERO.insight-5.5.6.zip && \
echo TODO: rm OMERO.insight-5.5.6.zip

RUN mkdir .java && \
cd OMERO.insight-5.5.6 && \
wget -q https://www.openmicroscopy.org/img/logos/omero-logomark.svg
# https://developer.gnome.org/desktop-entry-spec/
#COPY --chown=${NB_UID}:${NB_GID} *.desktop /home/jovyan/Desktop/
COPY --chown=1000:100 *.desktop /home/jovyan/Desktop/
# Configure default OMERO.insight server list
#COPY --chown=${NB_UID}:${NB_GID} java_userPrefs .java/.userPrefs
COPY --chown=1000:100 java_userPrefs .java/.userPrefs

WORKDIR ${HOME}

# Both these should work:


+ 14
- 0
Fiji.desktop View File

@@ -0,0 +1,14 @@
[Desktop Entry]
Version=1.0
Name=Fiji Is Just ImageJ
GenericName=Fiji Is Just ImageJ
X-GNOME-FullName=Fiji Is Just ImageJ
Comment=Scientific Image Analysis
Type=Application
Categories=Education;Science;ImageProcessing;
Exec=/home/jovyan/Fiji.app/ImageJ-linux64
TryExec=/home/jovyan/Fiji.app/ImageJ-linux64
Terminal=false
StartupNotify=true
Icon=/home/jovyan/Fiji.app/images/icon.png
StartupWMClass=fiji-Main

+ 29
- 0
LICENSE View File

@@ -0,0 +1,29 @@
BSD 3-Clause License

Copyright (c) 2019, University of Dundee
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

+ 13
- 0
OMERO.insight.desktop View File

@@ -0,0 +1,13 @@
[Desktop Entry]
Version=1.0
Name=OMERO.insight
GenericName=OMERO.insight
X-GNOME-FullName=OMERO.insight
Comment=OMERO desktop client
Type=Application
Categories=Education;Science;ImageProcessing;
Exec=/home/jovyan/OMERO.insight-5.5.6/bin/omero-insight
TryExec=/home/jovyan/OMERO.insight-5.5.6/bin/omero-insight
Terminal=false
StartupNotify=true
Icon=/home/jovyan/OMERO.insight-5.5.6/omero-logomark.svg

+ 7
- 6
README.md View File

@@ -1,12 +1,13 @@
# Jupyter Linux Desktop
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gist/manics/7d1f4b76ce06c2bb07db88e3496a1561/master?urlpath=desktop)
# Jupyter OMERO client Desktop
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/manics/jupyter-omeroanalysis-desktop/master?urlpath=Desktop)

Example of running a Linux desktop or window manager with noVNC inside Jupyter.
Run OMERO clients in a Linux desktop using Jupyter.

This is based on https://github.com/ryanlovett/nbnovnc

```
docker build -t jupyter-desktop .
docker run -it --rm -p 8888:8888 jupyter-desktop jupyter notebook --debug
docker build -t jupyter-omeroanalysis-desktop .
docker run -it --rm -p 8888:8888 jupyter-omeroanalysis-desktop
```
Go to `/desktop` e.g. http://localhost:8888/desktop and if you're lucky you'll see the desktop you installed.

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.

+ 3
- 0
java_userPrefs/org/openmicroscopy/prefs.xml View File

@@ -0,0 +1,3 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0"/>

+ 3
- 0
java_userPrefs/org/openmicroscopy/shoola/prefs.xml View File

@@ -0,0 +1,3 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0"/>

+ 3
- 0
java_userPrefs/org/openmicroscopy/shoola/util/prefs.xml View File

@@ -0,0 +1,3 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0"/>

+ 7
- 0
java_userPrefs/org/openmicroscopy/shoola/util/ui/login/prefs.xml View File

@@ -0,0 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0">
<entry key="omeroConnectionSpeed" value="0"/>
<entry key="omeroServer" value="nightshade.openmicroscopy.org:4064,outreach.openmicroscopy.org:4064,idr.openmicroscopy.org:4064,demo.openmicroscopy.org:4064"/>
<entry key="omeroTransferEncrypted" value="true"/>
</map>

+ 3
- 0
java_userPrefs/org/openmicroscopy/shoola/util/ui/prefs.xml View File

@@ -0,0 +1,3 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0"/>

+ 3
- 0
java_userPrefs/org/prefs.xml View File

@@ -0,0 +1,3 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0"/>

+ 1
- 1
jupyter_notebook_config.py View File

@@ -9,7 +9,7 @@ else:

vnc_socket = os.path.join(os.getenv('HOME'), '.vnc', 'socket')
c.ServerProxy.servers = {
'desktop': {
'Desktop': {
'command': [
'/opt/conda/bin/websockify',
'-v',


Loading…
Cancel
Save