Merge pull request #5 from jburel/binder

Binder

README.md

@@ -1,9 +1,28 @@
-# This is a template useful to create guides
+# User guide for Fiji and OMERO
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks)
+
+
+This guide demonstrates how to analyze data stored in OMERO in Fiji.
+This can be done using the User Interface or via the scripting facility in Fiji.
+
+
+To run the notebooks, you can either [run on mybinder.org](https://mybinder.org/v2/gh/ome/omero-guide-fiji/master?filepath=notebooks) or build locally with [repo2docker](https://repo2docker.readthedocs.io/).
+
+To build locally:
+
+ * Install [Docker](https://www.docker.com/) if required
+ * Create a virtual environment and install repo2docker from PyPI.
+ * Clone this repository
+ * Run  ``repo2docker``. 
+ * Depending on the permissions, you might have to run the command as an admin
+
+```
+pip install jupyter-repo2docker
+git clone https://github.com/ome/omero-guide-fiji.git
+cd omero-guide-fiji
+repo2docker .
+```
 
 This a Sphinx based documentation. 
 If you are unfamiliar with Sphinx, we recommend that you first read 
 [Getting Started with Sphinx](https://docs.readthedocs.io/en/stable/intro/getting-started-with-sphinx.html).
-
-When creating a new repository, this template could be used.
-
-The value in ``conf.py`` should be replaced by the name of your project.

binder/apt.txt

@@ -0,0 +1,15 @@
+bsdtar
+curl
+dbus-x11
+firefox
+less
+net-tools
+openjdk-8-jre
+unzip
+vim
+xfce4
+xfce4-panel
+xfce4-session
+xfce4-settings
+xorg
+xubuntu-icon-theme 

binder/environment.yml

@@ -0,0 +1,13 @@
+name: base
+channels:
+  - conda-forge
+  - ome
+  - manics
+dependencies:
+  - beakerx
+  - pip
+  - websockify=0.9.0
+  - pip:
+    # Recent jupyter-server-proxy to load vnc_lite.html instead of /
+    # https://github.com/jupyterhub/jupyter-server-proxy/pull/151
+    - https://github.com/jupyterhub/jupyter-server-proxy/archive/0e67e1afd0bab1342443f13bd147a2f8c682e9e0.zip

binder/postBuild

@@ -0,0 +1,63 @@
+#!/bin/bash
+set -eux
+
+env
+
+VNC_APPLICATION_DIR=$CONDA_DIR/vnc
+mkdir $VNC_APPLICATION_DIR
+pushd $VNC_APPLICATION_DIR
+
+# Novnc: just want web files
+curl -sSfL https://github.com/novnc/noVNC/archive/v1.1.0.tar.gz | tar -zxf -
+
+# Patch novnc to use correct path to websockify (defaults to /)
+# Note if you use vnc.html you will need to patch ui.js to use the correct path
+# and also to override localstorage which may store an incorrect path from a
+# different session
+# Also resize server instead of scaling client
+sed -i.bak \
+    -e "s%\('path', 'websockify'\)%'path', window.location.pathname.replace(/[^/]*$/, '').substring(1) + 'websockify'); console.log('websockify path:' + path%" \
+    -re "s%rfb.scaleViewport = .+%rfb.resizeSession = readQueryVariable('resize', true);%" \
+    noVNC-1.1.0/vnc_lite.html
+
+# Install tigervnc
+curl -sSfL 'https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.9.0.x86_64.tar.gz' | tar -zxf - --strip=2
+
+
+cp $REPO_DIR/jupyter_desktop/share/xstartup .
+chmod +x xstartup
+
+
+# Desktop applications
+# Fiji and OMERO insight
+
+OMERO_INSIGHT_VERSION=5.5.11
+OMERO_INSIGHT_URL_BASE=https://github.com/ome/omero-insight/releases/download/v$OMERO_INSIGHT_VERSION
+
+wget https://downloads.imagej.net/fiji/latest/fiji-nojre.zip
+unzip -q fiji-nojre.zip
+rm fiji-nojre.zip
+
+
+pushd Fiji.app/plugins
+wget -q $OMERO_INSIGHT_URL_BASE/omero_ij-$OMERO_INSIGHT_VERSION-all.jar
+popd
+
+mkdir Desktop
+
+# Copy the script to the Desktop
+cp -R $REPO_DIR/scripts Desktop
+
+cp $REPO_DIR/jupyter_desktop/share/*.desktop Desktop
+chmod +x Desktop/*.desktop
+
+popd
+
+pushd $REPO_DIR/jupyter_desktop
+
+# Configure jupyter-server-proxy VNC
+# https://jupyter-server-proxy.readthedocs.io/en/latest/server-process.html#specifying-config-from-python-packages
+pip install .
+python -c "from pkg_resources import iter_entry_points; print(list(iter_entry_points(group='jupyter_serverproxy_servers')))"
+
+popd

binder/start

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -eux
+
+export DISPLAY=:1.0
+ln -s "$CONDA_DIR/vnc/Desktop"
+
+exec "$@"

jupyter_desktop/jupyter_desktop.py

@@ -0,0 +1,26 @@
+import os
+
+
+def setup_desktop():
+    VNC_APPLICATION_DIR = os.path.join(os.getenv('CONDA_DIR'), 'vnc')
+    return {
+        'command': [
+            'websockify', '-v',
+            '--web', VNC_APPLICATION_DIR + '/noVNC-1.1.0',
+            '--heartbeat', '30',
+            '5901',
+            '--unix-target', VNC_APPLICATION_DIR + '/socket',
+            '--',
+            VNC_APPLICATION_DIR + '/bin/vncserver',
+            '-verbose',
+            '-xstartup', VNC_APPLICATION_DIR + '/xstartup',
+            '-geometry', '1024x768',
+            '-SecurityTypes', 'None',
+            '-rfbunixpath', VNC_APPLICATION_DIR + '/socket',
+            '-fg',
+            ':1',
+        ],
+        'port': 5901,
+        'timeout': 30,
+        'mappath': {'/': '/vnc_lite.html'},
+    }

jupyter_desktop/setup.py

@@ -0,0 +1,17 @@
+import setuptools
+
+
+setuptools.setup(
+    name="jupyter-desktop-server",
+    # py_modules rather than packages, since we only have 1 file
+    py_modules=['jupyter_desktop'],
+    entry_points={
+        'jupyter_serverproxy_servers': [
+            'desktop = jupyter_desktop:setup_desktop',
+        ]
+    },
+    install_requires=['jupyter-server-proxy'],
+    package_data={
+        'jupyter_desktop': ['desktop/*'],
+    },
+)

jupyter_desktop/share/Fiji.desktop

@@ -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=/srv/conda/vnc/Fiji.app/ImageJ-linux64
+TryExec=/srv/conda/vnc/Fiji.app/ImageJ-linux64
+Terminal=false
+StartupNotify=true
+Icon=/srv/conda/vnc/Fiji.app/images/icon.png
+StartupWMClass=fiji-Main

jupyter_desktop/share/xstartup

@@ -0,0 +1,2 @@
+#!/bin/sh
+exec /usr/bin/dbus-launch xfce4-session