Code Ocean capsules need a run script set to run. 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, often called run or run.sh, 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. Last, 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 shell scripts. Their course on automation and make may also be of interest. 

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