All Code Ocean capsules come with a run.sh  script by default. These are shell scripts, typically written in Bash. Shell scripts execute system-level operations. Browsing Code Ocean's Explore page, you will see that many capsules retain some version of this file adapted to each capsule.


On Code Ocean, shell scripts are often used as master scripts, because they can link together multiple analysis steps, including operations in multiple languages. Shell scripts are also necessary for providing command line inputs, which underpin every Code Ocean interface.  Lastly, shell scripts provide useful commands for moving and saving files, such as creating symbolic links between folders.

How to learn:

Software Carpentry provides an excellent course on their many use cases. Their course on automation and make may also be of interest.

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