Explain the connection between packages, containers and Galaxy#80
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Explain the connection between packages, containers and Galaxy#80
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Polished notes from introduction given by Björn
anuprulez
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Apr 8, 2026
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| **conda-forge** | ||
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| On the conda-forge side, there is a dedicated github repo for development of each individual package recipe. |
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| On the conda-forge side, there is a dedicated github repo for development of each individual package recipe. | |
| On the conda-forge side, there is a dedicated github repository for development of each individual package recipe. |
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| **bioconda** | ||
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| The bioconda community has organized all of their channel's package recipes as folders within a single github repo at https://github.com/bioconda/bioconda-recipes. |
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| The bioconda community has organized all of their channel's package recipes as folders within a single github repo at https://github.com/bioconda/bioconda-recipes. | |
| The bioconda community has organized all of their channel's package recipes as folders within a single github repository at https://github.com/bioconda/bioconda-recipes. |
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| overview provided by @bgruening | ||
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| for an overview picture, see: https://github.com/BioContainers/singularity-build-bot/blob/master/README.md#broader-context |
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| for an overview picture, see: https://github.com/BioContainers/singularity-build-bot/blob/master/README.md#broader-context | |
| For an overview picture, see: https://github.com/BioContainers/singularity-build-bot/blob/master/README.md#broader-context |
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| # Conda, (Bio)Containers and Galaxy | |||
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| overview provided by @bgruening | |||
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| overview provided by @bgruening | |
| Overview provided by @bgruening |
| - Can build containers (docker or singularity ones) from any kind of software package, but only the conda packaging format is relevant for this topic. | ||
| - involucro is configurable through lua extension scripts | ||
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| 2. conda |
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| 2. conda | |
| 2. Conda |
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| Once a pull request against any conda-forge package's development repo gets accepted, a new version of that package gets built and deposited under the conda-forge channel at anaconda.org. No further building of artifacts happens on the conda-forge side. | ||
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| **bioconda** |
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| **bioconda** | |
| **Bioconda** |
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| The bioconda contribution workflow is described at https://bioconda.github.io/. | ||
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| When a pull request against the bioconda-recipes repo gets merged, packages touched by the PR get built and deposited under the bioconda channel at anaconda.org. |
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| When a pull request against the bioconda-recipes repo gets merged, packages touched by the PR get built and deposited under the bioconda channel at anaconda.org. | |
| When a pull request against the bioconda-recipes repository gets merged, packages touched by the PR get built and deposited under the bioconda channel at anaconda.org. |
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| for an overview picture, see: https://github.com/BioContainers/singularity-build-bot/blob/master/README.md#broader-context | ||
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| but lets start from the beginning. |
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| but lets start from the beginning. | |
| but let's start from the beginning. |
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| 2. conda | ||
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| A programming language and OS-agnostic package management sytem. |
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| A programming language and OS-agnostic package management sytem. | |
| A programming language and OS-agnostic package management system. |
| - checks against quay.io to see if a mulled container image with this hash already exists | ||
| - if not, creates pull requests against the biocontainers/multi-package-containers under the bot account @dockerhub-toolshed. | ||
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| These PRs do not touch the combinations/hash.tsv file like manually created PRs, but instead create a dedicated file per container, like e.g. [here](https://github.com/BioContainers/multi-package-containers/pull/3899/changes), but when they get merged the cause docker and singularity image uploads like for manually created PRs. |
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but when they get merged the cause docker and singularity image uploads like for manually created PRs.
the statement is not so clear.
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Polished notes from introduction given by Björn.