Samtools with BCFtools, for sorting and indexing aligned reads and calling variants from them.
This image is the default image of samtools (ghcr.io/randomcontainers/samtools:latest), published under its own name. The contents are the same; the digests differ. It contains Samtools and BCFtools, on Ubuntu or Alpine, for linux/amd64 and linux/arm64.
These are unofficial builds, not affiliated with or endorsed by the upstream projects. Report problems with the image in randomcontainers/samtools and problems with a tool itself in that tool's own issue tracker.
docker run --rm --user "$(id -u):$(id -g)" -v "$PWD:/work" ghcr.io/randomcontainers/samtools-bcftools sort -o sorted.bam --write-index in.bamThe examples in the samtools README work with this image too.
<version> is the Samtools version.
| Tags | Base |
|---|---|
latest, <version>, ubuntu, <version>-ubuntu, <version>-ubuntu26.04 |
Ubuntu 26.04 |
alpine, <version>-alpine, <version>-alpine3.24 |
Alpine 3.24 |
latest and <version> are the Ubuntu 26.04 images. The images are currently built on Ubuntu 26.04 and Alpine 3.24. Tags without a distro version move to the next distro release when the project does; tags ending in ubuntu26.04 or alpine3.24 stay on that release and are no longer rebuilt once the project moves to the next one.
Only the tags of the Samtools version currently in samtools's package.yml are rebuilt, exact-version tags included, so pin a digest when you need the same bytes every time. Tags of older versions stay as they were last built. The published tags and their digests are listed on the package page.
linux/amd64 and linux/arm64, both built natively on GitHub-hosted runners.
The working directory is /work. The image runs as UID 1000, and any other UID works too: HOME is then /, and caches go to /cache, which anyone can write to. How to get output files owned by you depends on how you run containers:
| Runtime | Flag |
|---|---|
| Docker on Linux (rootful), GitHub Actions | --user "$(id -u):$(id -g)" |
| Rootless Podman | --userns=keep-id |
| Rootless Docker | --user 0:0 (root in the container is your user on the host) |
| Docker Desktop on macOS or Windows | none, file ownership is mapped for you |
| Package | License | Repository |
|---|---|---|
| Samtools | MIT AND BSD-3-Clause AND BSD-2-Clause AND CC0-1.0 AND LicenseRef-Public-Domain |
randomcontainers/samtools |
| BCFtools | MIT AND BSD-3-Clause AND BSD-1-Clause AND CC0-1.0 AND LicenseRef-Public-Domain |
randomcontainers/bcftools |
Each image has a build provenance attestation from this repository's GitHub Actions run. The run uses the shared build workflow of randomcontainers/ci, which signs the attestation, so name both repositories:
gh attestation verify oci://ghcr.io/randomcontainers/samtools-bcftools:latest \
--repo randomcontainers/samtools-bcftools --signer-repo randomcontainers/ciImages from ghcr.io/randomcontainers/samtools are built in randomcontainers/samtools, so verify them with --repo randomcontainers/samtools --signer-repo randomcontainers/ci.
The images are rebuilt when a new image of a package above is published, for example after an upstream release. They are also rebuilt when the base image changes and at least every 7 days, so distro security fixes reach the current tags. The package repositories describe how each upstream release is picked up.
The image contents are licensed under MIT AND BSD-3-Clause AND BSD-2-Clause AND CC0-1.0 AND LicenseRef-Public-Domain AND BSD-1-Clause. The version of each package is in /usr/local/share/randomcontainers/<package>/version and its license files are in /usr/local/share/randomcontainers/<package>/licenses/.
Ubuntu and Alpine packages keep their own licenses. The SBOM of each platform image lists them with their versions:
docker buildx imagetools inspect ghcr.io/randomcontainers/samtools-bcftools:latest --format '{{ json .SBOM }}'The files in this repository are available under the MIT license, see LICENSE.
To suggest another tool, use the Request a tool form.
The files here are generated from the combos section of package.yml in randomcontainers/samtools. Open issues and pull requests there.