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@@ -15,17 +15,13 @@ See the [Smaller containers](https://www.informaticsmatters.com/category/contain
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For each RDKit version (image tag) we build a number of images:
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*[informaticsmatters/rdkit-build-debian](https://hub.docker.com/r/informaticsmatters/rdkit-build-debian/) - this does a full build of RDKit from source. The result is a kitchen sink image (almost 2GB in size) that contains the entire build infrastructure and eveything that is built. The main purpose of this image is to build the artifacts needed for assembling the other lightweight images. Whist this image might be of some use for personal hacking it is NOT suitable for a public facing system as it is so large and has such a big attack surface. Earlier versions were named `informaticsmatters/rdkit-build`. NOTE: we have stopped pushing this image as it is large and not very useful.
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*[informaticsmatters/rdkit-python-debian](https://hub.docker.com/r/informaticsmatters/rdkit-python-debian/) - a Debian based distribution designed for running RDKit from Python 2. The image size is approx 400MB. The last Python 2 images are for the `Release_2018_09` release.
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*[informaticsmatters/rdkit-python3-debian](https://hub.docker.com/r/informaticsmatters/rdkit-python3-debian/) - a Debian based distribution designed for running RDKit from Python 3. These images start from the `Release_2019_03` release.
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*[informaticsmatters/rdkit-java-debian](https://hub.docker.com/r/informaticsmatters/rdkit-java-debian/) - a Debian based distribution designed for running RDKit from Java.
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*[informaticsmatters/rdkit-tomcat-debian](https://hub.docker.com/r/informaticsmatters/rdkit-tomcat-debian/) - a Debian based distribution designed for running a servlet in Apache Tomcat that uses the RDKit Java bindings. You need to provide the war file with the web application.
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*[informaticsmatters/rdkit-cartridge-debian](https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian/) - a Debian based distribution with PostgreSQL and the RDKit cartridge. Note that we were unable to build cartridge images for the 2021_09 and 2022_03 based releases.
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*[informaticsmatters/rdkit-build-centos](https://hub.docker.com/r/informaticsmatters/rdkit-build-centos/) - Kitchen sink build image equivalent to `informaticsmatters/rdkit-build-debian`.
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*[informaticsmatters/rdkit-python3-centos](https://hub.docker.com/r/informaticsmatters/rdkit-python3-centos/) - a Centos based distribution designed for running RDKit from Python 3. Thes images start from the `Release_2019_09` release.
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*[informaticsmatters/rdkit-java-centos](https://hub.docker.com/r/informaticsmatters/rdkit-java-centos/) - a Centos based distribution designed for running RDKit from Java.
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Note: we primarily focus on the Debian based images. Other platforms are not so well maintained.
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Note: we now focus on the Debian based images. In the past we also built on centos and fedora, but this caused too much
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of a maintenance problem.
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## Branches
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*`Release_2023_03_2` - build from RDKit Release_2023_03_2 release tag. These images should never change [1]. Images have tag of `Release_2023_03_2`
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[1] Where we say that the images should never change what we really mean in that the RDKit content should never change. We may rebuild these images occasionally when we find further improvements, and the underlying Centos/Debian packages may be updated, but the RDKit code should be exactly the same.
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[1] Where we say that the images should never change what we really mean in that the RDKit content should never change.
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We may rebuild these images occasionally when we find further improvements, and the underlying Debian packages may be
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updated, but the RDKit code should be exactly the same.
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[2] These images were originally tagged as `Release_2018_03_01` (2 digits as the final number). For better consistency with the RDKit GitHub tag names we switched to using a single digit format. Tags with two digits are also present for backward compatibility and point to the equivalent single digit image. Please use the single digit format.
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[2] These images were originally tagged as `Release_2018_03_01` (2 digits as the final number). For better consistency
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with the RDKit GitHub tag names we switched to using a single digit format. Tags with two digits are also present for
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backward compatibility and point to the equivalent single digit image. Please use the single digit format.
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GitHub repo for RDKit is [here](https://github.com/rdkit/rdkit).
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GitHub repo for this project is [here](https://github.com/InformaticsMatters/docker-rdkit)
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To create images for a new version of RDKit you should only need to create a new branch from `master` and then edit `params.sh`.
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To create images for a new version of RDKit you should only need to create a new branch from the corresponding
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previous version and then edit `params.sh`.
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## Build and run
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Since October 2023 we have switched to a multi-stage build and are building images for amd64 and arm64 architectures.
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Thanks to @nmunro and @artran for assistance with building on arm64.
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Thanks to @nmunro and @artran for assistance with building on arm64. These arm64 images should be treated as
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experimental. Please report any issue you may find.
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You need to use the `buildx` extensions to build these images. The Dockerfile-debian is the multi-stage Dockerfile
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that builds all the images, and it is run by executing `build-debian.sh`, which is parameterised through the contents
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of `params.sh`.
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The `build` stage builds RDKit form the appropriate GitHub branch for RDKit, and creates the deb packages and the Java
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artifacts from it for use in the `python`, `java`, `tomcat` and `cartridge` stages.
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Each subsequent stage is run separately and the images pushed to dockerhub. Note: only the amd64 is currently built for
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the `tomcat` image.
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Each subsequent stage is run separately and the images pushed to dockerhub.
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Note: only the amd64 is currently built for the `tomcat` image.
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Run the Python image like this:
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@@ -178,11 +180,11 @@ rdkit=# \q
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Notes:
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1. You must initially connect to the database as the `postgres` user, hence the need for the `-u postgres` option for the `docker exec` command.
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1. You must initially connect to the database as the `postgres` user, hence the need for the `-u postgres` option for
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