Spike Interface container with jupyterlab interface (#1)

* Has a few standard spike sorters installed
* Can be used on any OS
* Has option to drag and drop data folder to start jupyterlab (for Windows users)

Author: vncntprvst

spikeinterface/Dockerfile

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+FROM jupyter/datascience-notebook:hub-1.5.0
+
+LABEL maintainer="Vincent Prevosto <prevosto@mit.edu>"
+
+USER root
+# APT packages
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    libgl1-mesa-glx \
+    datalad && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# copy repo
+WORKDIR /srv
+RUN git clone https://github.com/SpikeInterface/spikeinterface.git
+
+RUN fix-permissions $CONDA_DIR && \
+fix-permissions /home/$NB_USER && \
+fix-permissions /srv/spikeinterface
+
+#Switch to user
+USER $NB_UID
+
+# update Anaconda and install pip 
+RUN conda update -y conda && \
+     conda install -y pip
+
+# Conda installs
+RUN conda config --set channel_priority flexible && \
+    conda install -y -c conda-forge nb_conda_kernels \
+    jupyter_contrib_nbextensions \
+    jupyterlab-git \
+    pynwb && \
+    conda clean -tipsy
+
+# Create environment
+RUN ln -s /srv/spikeinterface /home/$NB_USER/
+WORKDIR /home/$NB_USER/spikeinterface/installation_tips/
+RUN conda env create -f full_spikeinterface_environment_mac.yml
+
+# Make kernels available
+SHELL ["conda","run","-n","spikeinterface","/bin/bash","-c"]
+RUN conda install --quiet --yes ipykernel && \
+    conda install --quiet --yes -c conda-forge datalad && \
+    python -m ipykernel install --user --name spikeinterface --display-name "spikeinterface" && \
+    pip install jupytext dotenv
+
+# Configure git (required by datalad)
+WORKDIR /home/$NB_USER/spikeinterface/
+RUN git config --global --add user.name "Jovyan" && \
+    git config --global --add user.email jovyan@example.net
+
+# Create "getting started" notebook in home directory
+WORKDIR /home/$NB_USER/spikeinterface/examples/getting_started/
+RUN jupytext --to notebook plot_getting_started.py && \
+    cp ~/spikeinterface/examples/getting_started/plot_getting_started.ipynb ~/getting_started.ipynb
+
+# Make sure to switch back to user (avoid running ui containers as root)
+USER $NB_UID
+WORKDIR /home/$NB_USER

spikeinterface/Run_SpikeInterface.bat

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+@echo off
+Title Drag and drop a data folder
+Mode con cols=60 lines=3
+IF [%1] EQU [] Goto:Error
+set JUPYTER_TOKEN=mytoken
+docker run -d --rm --name spikeinterface -v "%~1":/home/jovyan/data -p 8888:8888 -e JUPYTER_TOKEN wanglabneuro/spikeinterface:0.1
+TIMEOUT /T 2
+START /W "" http://localhost:8888/lab?token=mytoken
+ECHO Spike Interface started
+TIMEOUT /T 2
+Exit /b
+
+::**********************************************************
+:Error
+Color 0C & echo(
+ECHO    You must drag and drop a folder on this batch program 
+Timeout /T 5 /NoBreak >nul
+Exit /b
+::**********************************************************

spikeinterface/build.sh

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+#!/bin/bash
+
+docker build -t wanglabneuro/spikeinterface:0.1 .

spikeinterface/readme.md

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+### How to build this image
+Open a terminal, navigate to the spikeinterface directory, then run:   
+`docker build -t wanglabneuro/spikeinterface:0.1 .`  
+On Linux systems, you can also use the build script (after making it executable `chmod +x build.sh`):    
+`./build.sh`  
+
+### How to run the spikeinterface container
+**Method 1** For Windows: drag and drop the data folder on `Run_SpikeInterface.bat`. Replace "mytoken" by whatever word.   
+  
+**Method 2**
+On Linux/MacOS:  
+`export JUPYTER_TOKEN='mytoken'`
+`docker run -d --rm --name spikeinterface -v "${PWD}":/home/jovyan/work -p 8888:8888 -e JUPYTER_TOKEN wanglabneuro/spikeinterface:0.1`  
+
+On Windows:  
+`set JUPYTER_TOKEN=mytoken`
+`docker run -d --rm --name spikeinterface -v "%CD%":/home/jovyan/work -p 8888:8888 -e JUPYTER_TOKEN wanglabneuro/spikeinterface:0.1`  
+  
+Then open http://localhost:8888/lab?token=mytoken in a browser.
+
+
+
+