Dockerfile to build a server with Jupyterhub and RStudio, ready for Python, R and Julia languages.
-
Jupyterhub [https://github.com/jupyter/jupyterhub] with support for the following languages:
-
Python 2.7
-
Python 3.5
-
R 3.2.3
-
Julia 0.4
-
-
RStudio Server [https://www.rstudio.com/]
-
Shiny Server [https://www.rstudio.com/products/shiny/shiny-server2/]
To build the image, run the following comand:
# docker build -t math-server .
To start the server, use:
# docker run -d -p 8787:8787 -p 8000:8000 --name ms1 math-server
The default ports are:
* 8787 for RStudio
* 8000 for Jupyter
Docker [https://www.docker.com/].
Data files are at /usr/local/share/jupyter/hub.
To start the server:
# jupyterhub
By default, will be accessible on the following link: http://localhost:8000, and will create state files (jupyterhub_cookie_secret, jupyterhub.sqlite) on current directory, and use default configuration.
You can generate a sample configuration file with:
# jupyterhub --generate-config
To start the server using a configuration file, use:
# jupyterhub -f jupyterhub_config.py
To set IP and port, use:
# jupyterhub --ip=192.168.1.2 --port=443
You may have to open port for external access:
# /sbin/iptables -I INPUT -p tcp -m tcp --dport 8000 -j ACCEPT
# /sbin/service iptables save
For https support, add the following lines to the config file:
c.JupyterHub.port = 443
c.JupyterHub.ssl_cert = '/root/.ssh/sample-cert.pem'
c.JupyterHub.ssl_key = '/root/.ssh/sample-key.pem'443 is the default port for https. So the server will be accessible using https://localhost.
sample-cert.pem is the signed certificate file, and sample-key.pem is the private ssl key.
You can generate self signed certificate file with:
mkdir ~/.ssh
openssl req -x509 -newkey rsa:2048 -keyout ~/.ssh/sample-key.pem -out ~/.ssh/sample-cert.pem -days 9999 -nodes -subj "/C=BR/ST=Rio de Janeiro/L=Rio de Janeiro/O=org/OU=unit/CN=website"
chmod 400 sample*.pem
But be aware that your browser will not recognize the certificate as trusted.
Configuration files are at /etc/rstudio.
Default port is 8787.
Change the default port by editing rserver.conf. The following will change to port 80:
# echo -e "www-port=80" | tee /etc/rstudio/rserver.conf
# rstudio-server restart
# rstudio-server verify-installation
auth-pam-sessions-profile directive on /etc/rstudio.rserver.conf may not work. If that happens, RStudio will look at /etc/pam.d/rstudio.
Python
root user will add packages with pip2 or pip3 command line. Packages will be stored on /usr/local/lib/python2.7 or /usr/local/lib/python3.5 directories.
R
Check package locations with $ R -e '.libPaths()'.
System packages will be installed on /usr/lib64/R/library.
Each user can have a local package dir, automatically created under ~/R.
root user will add packages with R -e 'install.packages("pkg-name")' command.
Julia
System packages will be installed to /usr/local/julia/share/julia/site.
Each user can add new search directories by changing Julia's LOAD_PATH variable.
julia> LOAD_PATH
2-element Array{ByteString,1}:
"/usr/local/julia/local/share/julia/site/v0.4"
"/usr/local/julia/share/julia/site/v0.4"root user will add packages with julia -e 'Pkg.add("pkg-name")' command.
It's important to run using pkg-name after installation to precompile the packages. This will store files on /usr/local/share/julia/lib/v0.4/.
-
Jupyter main website: http://jupyter.org/
-
Jupyterhub Docs: https://jupyterhub.readthedocs.org/en/latest/index.html
-
Full list of supported kernels for Jupyter: https://github.com/ipython/ipython/wiki/IPython-kernels-for-other-languages
-
RStudio website: https://www.rstudio.com/
-
RStudio Server download page: https://www.rstudio.com/products/rstudio/download-server/
-
RStudio Server Admin Guide: https://s3.amazonaws.com/rstudio-server/rstudio-server-pro-0.99.879-admin-guide.pdf
-
Shiny Server Admin Guide: http://rstudio.github.io/shiny-server/latest/