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Getting Started

Getting Started

Covering: 1) what is a compute capsule 2) uploading code and data 3) configuring your environment, 4) publishing on Code Ocean.

Shahar Zaks avatar Seth Green avatar
12 articles in this collection
Written by Shahar Zaks and Seth Green

What is a compute capsule?

Code + (optional) data + computational environment = the minimum required for computational reproducibility.
Shahar Zaks avatar
Written by Shahar Zaks
Updated over a week ago
Uploading code and data

How do I upload my code to Code Ocean?

Uploading to Code Ocean for new users.
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Written by Seth Green
Updated over a week ago

Paths

/code, /data, /results, and symbolic links.
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Written by Seth Green
Updated over a week ago

Saving files

Files must be saved explicitly to the /results folder.
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Written by Seth Green
Updated over a week ago

Using public datasets

Take advantage of preloaded public datasets, or upload your own.
Shahar Zaks avatar
Written by Shahar Zaks
Updated over a week ago

What is, and is not, a good fit for publishing and sharing on Code Ocean?

Pipelines, analyses, visualizations, and statistical checks are all great fits for publishing on Code Ocean.
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Written by Seth Green
Updated over a week ago
The computational environment

Configuring your computational environment: an overview

Where to begin, and what steps to take next.
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Written by Seth Green
Updated over a week ago

Selecting a base environment

Choose from among a curated collection of runtime environments covering common languages and frameworks.
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Written by Seth Green
Updated over a week ago

The package management system

Install any libraries, packages, or dependencies your code needs in order to run.
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Written by Seth Green
Updated over a week ago

Using the postInstall script for further customization

Download, extract, compile – use the full set of tools available on Linux to set up your runtime environment.
Shahar Zaks avatar
Written by Shahar Zaks
Updated over a week ago

Monitoring and inspecting the result of the environment setup phase

The "buildLog" result file contains the console output from package installation commands and postInstall execution.
Seth Green avatar
Written by Seth Green
Updated over a week ago

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

How to use the package management system and postInstall script to install languages, interpreters, and compilers.
Shahar Zaks avatar
Written by Shahar Zaks
Updated over a week ago