Remove all parts that aren't just XFCE
- Move everything to base directory, since this repo is only for jupyter-desktop - Remove packages not needed for base functionality from apt.txt and environment.yml - Remove extra desktop shortcuts
This commit is contained in:
YuviPanda
parent
953b8e7139
commit
fdcd053cd3
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@ -1,14 +1,8 @@
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curl
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dbus-x11
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firefox
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less
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net-tools
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openjdk-8-jre
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unzip
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vim
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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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xubuntu-icon-theme
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@ -1,36 +0,0 @@
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name: napari
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channels:
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- conda-forge
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- manics
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dependencies:
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- python=3.6
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- pip
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- websockify=0.9.0
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- zeroc-ice-python=3.6.5
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# https://github.com/napari/napari/blob/v0.2.2/requirements/default.txt
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- dask
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- zarr
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- fsspec
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- imageio
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- ipykernel
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- numpy
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- qtpy
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- qtconsole
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- scipy
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- scikit-image
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- vispy
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- ipython
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- backcall
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- pyopengl
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- pyside2
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- wrapt
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- numpydoc
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- pip:
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# Recent 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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- https://github.com/jupyterhub/jupyter-server-proxy/archive/0e67e1afd0bab1342443f13bd147a2f8c682e9e0.zip
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- https://github.com/ome/omero-py/archive/v5.6.dev1.zip
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# The conda pyside2 package doesn't appear in pip list so napari tries to reinstall it
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# https://github.com/conda-forge/pyside-feedstock/issues/35
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# napari==0.2.2
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# Manually install in postBuild instead with --no-dependencies
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@ -1,74 +0,0 @@
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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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# 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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# 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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cp $REPO_DIR/jupyter_desktop/share/xstartup .
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chmod +x xstartup
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# Desktop applications
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# Fiji and OMERO insight
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#OMERO_INSIGHT_VERSION=5.5.6
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#OMERO_INSIGHT_URL_BASE=https://github.com/ome/omero-insight/releases/download/v$OMERO_INSIGHT_VERSION/
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OMERO_INSIGHT_VERSION=5.5.7-SNAPSHOT
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OMERO_INSIGHT_URL_BASE=https://users.openmicroscopy.org.uk/~spli/insight
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wget -q https://downloads.imagej.net/fiji/latest/fiji-nojre.zip
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unzip -q fiji-nojre.zip
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rm fiji-nojre.zip
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pushd Fiji.app/plugins
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wget -q $OMERO_INSIGHT_URL_BASE/OMERO.imagej-$OMERO_INSIGHT_VERSION.zip
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unzip -q OMERO.imagej-$OMERO_INSIGHT_VERSION.zip
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rm OMERO.imagej-$OMERO_INSIGHT_VERSION.zip
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popd
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wget -q $OMERO_INSIGHT_URL_BASE/OMERO.insight-$OMERO_INSIGHT_VERSION.zip
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unzip -q OMERO.insight-$OMERO_INSIGHT_VERSION.zip
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rm OMERO.insight-$OMERO_INSIGHT_VERSION.zip
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pushd OMERO.insight-$OMERO_INSIGHT_VERSION && \
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wget -q https://www.openmicroscopy.org/img/logos/omero-logomark.svg
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popd
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ln -s OMERO.insight-$OMERO_INSIGHT_VERSION OMERO.insight
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mkdir Desktop
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cp $REPO_DIR/jupyter_desktop/share/*.desktop Desktop
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chmod +x Desktop/*.desktop
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popd
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pushd $REPO_DIR/jupyter_desktop
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# Configure jupyter-server-proxy VNC
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# https://jupyter-server-proxy.readthedocs.io/en/latest/server-process.html#specifying-config-from-python-packages
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pip install .
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python -c "from pkg_resources import iter_entry_points; print(list(iter_entry_points(group='jupyter_serverproxy_servers')))"
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popd
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# Napari (dependencies already installed using conda)
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pip install --no-dependencies napari==0.2.2
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@ -0,0 +1,6 @@
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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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[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=/srv/conda/vnc/Fiji.app/ImageJ-linux64
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TryExec=/srv/conda/vnc/Fiji.app/ImageJ-linux64
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Terminal=false
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StartupNotify=true
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Icon=/srv/conda/vnc/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=/srv/conda/vnc/OMERO.insight/bin/omero-insight
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TryExec=/srv/conda/vnc/OMERO.insight/bin/omero-insight
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Terminal=false
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StartupNotify=true
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Icon=/srv/conda/vnc/OMERO.insight/omero-logomark.svg
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66
napari.ipynb
66
napari.ipynb
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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Napari\n",
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"\n",
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"\n",
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"## Setup: start the [desktop](../desktop)\n",
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"The link should open in a different window. If you see an error message try refreshing the window.\n",
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"\n",
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"Then run the first cell and wait for QT to be initialised before running the following cells. `Run all cells` will not work.\n",
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"\n",
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"If you are running this locally you should see some log messages. If you are running this on mybinder wait a few seconds before running the Napari cell. Note adding `time.sleep(5)` to the cell does not work!"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Use the novnc Desktop in the other window\n",
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"import os\n",
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"os.environ['DISPLAY'] = ':1.0'\n",
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"# instantiate Qt GUI\n",
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"%gui qt5"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import napari\n",
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"from skimage.data import astronaut\n",
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"\n",
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"# create the viewer on the Desktop and display the image\n",
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"viewer = napari.view_image(astronaut(), rgb=True)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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@ -0,0 +1,31 @@
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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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