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Merged
jeromekelleher merged 1 commit into from
Feb 5, 2026
Merged

Remove docker #2477

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12 changes: 0 additions & 12 deletions containers/docker-minimal
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20 changes: 0 additions & 20 deletions docs/development.md
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Expand Up @@ -795,26 +795,6 @@ Note the following tips:

- There is a script: `benchmarks/check_asv.sh` that can be used to benchmark recent commits.

## Containerization

To run msprime in a container, see the
{ref}`installation instructions <sec_installation_container>`.

You can use `docker` to locally build an image, but it requires root access:

```{code-block} bash

$ sudo docker build -t tskit/msprime .

```

[podman](<https://podman.io/>) can build and run images without root privilege.

```{code-block} bash

$ podman build -t tskit/msprime .

```
## Troubleshooting

- If `make` is giving you strange errors, or if tests are failing for
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113 changes: 1 addition & 112 deletions docs/installation.md
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# Installation

There are three options for installing `msprime`:
There are two main options for installing `msprime`:

1. {ref}`sec_installation_conda`: the recommended options for most users
2. {ref}`sec_installation_pip`: more flexibility and control for advanced users
3. {ref}`sec_installation_container`: to use
`msprime` inside an extremely isolated environment

(sec_installation_conda)=

Expand Down Expand Up @@ -233,112 +231,3 @@ With GSL installed, install from source by doing:
python3 -m pip install msprime --no-binary msprime
```

(sec_installation_container)=

## Via Container

An [open container](<https://opencontainers.org/>) image (aka docker image) is built on
[Dockerhub](<https://hub.docker.com/r/tskit/msprime>) for each release of
msprime. Each image is [tagged](<https://hub.docker.com/r/tskit/msprime/tags>)
with the corresponding release. For example, for msprime release 0.7.5, the
corresponding image tag is `tskit/msprime:0.7.5`.

To run a container, you can use [docker](<https://www.docker.com/>),
[Singularity](<https://sylabs.io/singularity/>),
[podman](<https://podman.io/>) or similar tools supporting docker images.

### docker

`docker` requires root privilege to run a container:

```{code-block} bash

$ sudo docker run -it tskit/msprime:<release> mspms 10 1 -T

```

### podman

podman can run an msprime container without root privilege:

```{code-block} bash

$ podman run -it docker.io/tskit/msprime:<release> mspms 10 1 -T

```

### Singularity

A docker image can also be converted to a Singularity container and
then run without root privilege:

```{code-block} bash

$ singularity pull docker://tskit/msprime:<release> msprime-<release>.simg
$ singularity exec msprime-<release>.simg mspms 10 1 -T

```

::::::{note}

It is possible that your current environment may conflict with the environment in the singularity container.
There are two workarounds:

1. Ignore your home with the conflicting environment with `--contain` or `-H </new/path/to/home> -e`

```{code-block} bash

$ singularity shell --contain msprime-release-0.7.3.simg
Singularity: Invoking an interactive shell within container...

Singularity msprime-release-0.7.3.simg:~> python3
Python 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import msprime
>>>

```

or use a different path as your home that does not have a conflicting environment

```{code-block} bash

$ singularity shell -H </new/path/to/home> -e msprime-release-0.7.3.simg
Singularity: Invoking an interactive shell within container...

Singularity msprime-release-0.7.3.simg:~/cnn_classify_demography> python3
Python 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import msprime
>>>

```

2. In python get rid of your local path

```{code-block} bash

$ singularity shell msprime-release-0.7.3.simg
Singularity: Invoking an interactive shell within container...

Singularity msprime-release-0.7.3.simg:~> python3
Python 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> for _path in sys.path:
... if ".local" in _path:
... sys.path.remove(_path)
...
>>> import msprime
>>>

```

::::::

For more information on Singularity, see <https://www.sylabs.io/guides/3.6/user-guide/>