Merge pull request #7 from jburel/binder

Binder

README.md

@@ -1,9 +1,27 @@
-# This is a template useful to create guides
+# Guide on how to integrate ilastik and OMERO
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks)
+
+This guide demonstrates how to use ilastik to analyze data stored in [IDR](https://idr.openmicroscopy.org/) or an OMERO server.
+
+This repository contains documentation and notebooks.
+
+To run the notebooks, you can either [run on mybinder.org](https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks) or build locally with [repo2docker](https://repo2docker.readthedocs.io/).
+
+To build locally:
+
+ * Install [Docker][https://www.docker.com/] if required
+ * Open a terminal as administrator
+ * Create a virtual environment and install repo2docker from PyPI.
+ * Clone this repository
+ * Run ``repo2docker``
+
+```
+pip install jupyter-repo2docker
+git clone https://github.com/ome/omero-guide-ilastik.git
+cd omero-guide-ilastik
+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 values in ``docs/conf.py`` should be replaced by the name of your project.

binder/apt.txt

@@ -0,0 +1 @@
+libgl1-mesa-glx

binder/environment.yml

@@ -0,0 +1,11 @@
+channels:
+  - conda-forge
+  - ome
+  - ilastik-forge
+dependencies:
+  - zeroc-ice36-python
+  - omero-py
+  - pip
+  - ilastik-dependencies-no-solvers
+  - ilastik-meta
+  - ipywidgets

binder/postBuild

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -eux
+
+chmod -R +x /srv/conda/envs/notebook/ilastik-meta

docs/index.rst

@@ -6,6 +6,6 @@ ilastik is a free open-source interactive learning and segmentation toolkit, wit
 Contents:
 
 .. toctree::
-   :maxdepth: 1
-
+   setup
    ilastik
+   :maxdepth: 1

docs/setup.rst

@@ -0,0 +1,61 @@
+Install ilastik and OMERO Python bindings
+==========================================
+
+In this section, we show how to install ilastik in a `Conda <https://conda.io/en/latest/>`_ environment.
+We will use the ilastik API to analyze data stored in an OMERO server.
+
+**Setup**
+---------
+
+We recommend to install the dependencies using Conda.
+Conda manages programming environments in a manner similar to 
+`virtualenv <https://virtualenv.pypa.io/en/stable/>`_.
+
+- Install `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ if necessary.
+
+- If you do not have a local copy of the `omero-guide-ilastik repository <https://github.com/ome/omero-guide-ilastik>`_, first clone the repository::
+
+    $ git clone https://github.com/ome/omero-guide-ilastik.git
+
+- Go into the directory::
+
+    $ cd omero-guide-ilastik
+
+- Create a programming environment using Conda::
+
+    $ conda create -n ilastik python=3.6
+
+- Install ilastik, its dependencies and ``omero-py`` in order to connect to an OMERO server using an installation file::
+
+    $ conda env update -n ilastik --file binder/environment.yml 
+
+- Activate the environment::
+
+    $ conda activate ilastik
+
+Alternatively you can create a local Docker Image using ``repo2docker``, see :download:`README.md <https://github.com/ome/omero-guide-ilastik/blob/master/README.md>`::
+
+    $ repo2docker .
+
+When the Image is ready:
+
+- Copy the URL displayed in the terminal in your favorite browser
+
+- Click the ``New`` button on the right-hand side of the window
+
+- Select ``Terminal``
+
+.. image:: images/terminal.png
+
+- A Terminal will open in a new Tab
+
+- A Conda environment has already been created when the Docker Image was built
+
+- To list all the Conda environment, run::
+
+    $ conda env list
+
+- The environment with ilastik and the OMERO Python bindings is named ``notebook``, activate it::
+
+    $ conda activate notebook
+