Setting up new or additional languages on Code Ocean via the package managers

Code Ocean offers many base environments with different languages pre-installed. The environment & configuration options can be used to install multiple languages in one compute capsule. Available package managers will suffice for many common languages less common languages will require a postInstall script.

Which environment should I start with?

• When not using a pre-installed language, use a base Ubuntu (18.04 or 16.04) environment

• When proprietary software, such as MATLAB or Stata is required, begin from an environment with proprietary language

• When using a GPU, select an environment with GPU access. These are labeled accordingly, or will reference CUDA or a deep learning framework

• For general flexibility, start from an image with Conda, these will include Python.

Installing a language using package managers:

The following are all available as apt-get packages:

• build-essential for the C/C++ toolchain (gcc/g++, make, etc.)

• r-base for R (note: r-base-dev will help you install R packages, adding a MRAN snapshot for R 3.4.4, which is what is available via apt-get is recommended

• octave for Octave

• python-pip for Python 2 and the pip installer

• python3-pip for Python 3 and the pip3 installer

• perl for Perl, add cpanm if necessary

• luajit for Lua add luarocks if necessary

• default-jdk for Java

• gfortran for Fortran

Once you add R or python, the commands Rscript or python will become available, respectively.

Installing langauges through Conda

If your base image has a conda installer, or if you add it via postInstall script, you can add languages and language-specific packages via supplemental conda channels.

• python is available by default, you can add python as a package, and specify the version for example 2.7.15 to install a different python version

• julia and lua are available through conda-forge

• r is available from channel r

Installing languages via the postInstall script:

See New and additional languages, toolboxes and compilers for examples such as D, GHDL, or gcc 7.

What if I need proprietary software that isn't currently supported?

Contact us at [e-mail] and we will be happy to look into it.