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README.md

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The BioCotnainers documentation is generated using readthedocs and sphinx. The final version of the documentations is deploy in: https://biocontainers-edu.readthedocs.io/en/latest/
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The BioContainers documentation is generated using readthedocs and sphinx. The final version of the documentation is deployed in: https://biocontainers-edu.readthedocs.io/en/latest/
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If you want to contribute with the documentation please do a Pull Request (PR) in the branch ``read_docs``.
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The documentation source files `.rst` are store in the **docs** folder.
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The documentation source files `.rst` are stored in the **docs** folder.
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If you want to build the project locally, you need to follow these steps:
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docs/introduction.rst

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Topics
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- Learn basic concepts of containers, docker and BioContainers
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- Learn basic concepts of containers, Docker and BioContainers
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- Get hands to create, deploy and use a BioContainers
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- Master the workflow for deploying and publishing a BioContainer in `Quay.io <https://quay.io/organization/biocontainers>`__ or `DockerHub <https://hub.docker.com/u/biocontainers/>`__
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- For technical questions related to containers (broken containers, container requests) `Containers Issues <https://github.com/BioContainers/containers/issues>`__ are preferred.
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If you find a typo or want to help us to make this tutorial even better, you are invited to click on "Improve this page".
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If you find a typo or want to help us to make this tutorial even better, you are invited to click on "Edit on GitHub".
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Concepts in this tutorial
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docs/what_is_container.rst

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.. note:: This simple command installs dia-umpire and all its dependencies
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Containers are built from existing operating systems. They are different from virtual machines because they don't posses an entire guest OS inside; instead, containers are built using optimized system libraries and use the host OS memory management and process controls. Containers normally are centralized around a specific software and you can make them executable by instantiating images from them.
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Containers are built from existing operating systems. They are different from virtual machines because they don't possess an entire guest OS inside; instead, containers are built using optimized system libraries and use the host OS memory management and process controls. Containers normally are centralized around a specific software and you can make them executable by instantiating images from them.
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.. image:: images/container.png
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:alt: What is Container
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:alt: What is a Container
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Why should I use a container?
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Most of the time when a bioinformatics analysis is performed, several bioinformatics tools and software should be installed and configured. This process can take several hours and demand a lot of effort including the installation of multiple dependencies and tools. BioContainers provide ready-to-use packages and tools that can be easily deployed and used on local machines, HPC and cloud architectures.
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Most of the time when a bioinformatics analysis is performed, several bioinformatics tools and software should be installed and configured. This process can take several hours and demands a lot of effort including the installation of multiple dependencies and tools. BioContainers provide ready-to-use packages and tools that can be easily deployed and used on local machines, HPC and cloud architectures.
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In the next video you can check out what you can achieve by using docker containers:
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Container technologies
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BioContainers has been built around three main technologies: **Conda**, **Docker** and **Singularity**. The BioContainers Community release for every bioinformatics software containers in these three technologies or flavours.
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BioContainers has been built around three main technologies: **Conda**, **Docker** and **Singularity**. The BioContainers Community releases for every bioinformatics software containers in these three technologies or flavours.
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.. note:: We do not provide detailed documentation about these three technologies because that can be found on their corresponding web sites, although we may explain some concepts important for understanding BioContainers as needed.
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