https://github.com/bast/apptainer-conda
Local Conda environments via Apptainer.
https://github.com/bast/apptainer-conda
apptainer conda containers micromamba singularity
Last synced: 7 months ago
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Local Conda environments via Apptainer.
- Host: GitHub
- URL: https://github.com/bast/apptainer-conda
- Owner: bast
- License: mit
- Created: 2021-11-25T00:26:30.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-11-06T00:40:39.000Z (11 months ago)
- Last Synced: 2025-01-28T02:32:43.553Z (9 months ago)
- Topics: apptainer, conda, containers, micromamba, singularity
- Homepage:
- Size: 19.5 KB
- Stars: 10
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Local Conda environments via [Apptainer](https://apptainer.org/)
The nice thing about this approach is that you don't need to install Conda and
you don't need to modify your environment/bashrc/settings.
I use it to install dependencies that may be tough to install on a
supercomputer or on my NixOS environment.
How to fetch the image:
```
$ apptainer pull https://github.com/bast/apptainer-conda/releases/download/0.7.0/conda.sif
```
## Usage
- Reads the Conda environment file
[environment.yml](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually).
- Creates the folder `environment`.
Run `myscript.py` inside the Conda environment defined by `environment.yml`:
```
$ ./conda.sif python myscript.py
```
Open Python shell inside the Conda environment defined by `environment.yml`:
```
$ ./conda.sif python
```
First time you run either of the above commands it will take a bit of time
since it needs to install the dependencies into the `environment` folder.
However, subsequent runs will start basically immediately since the environment
is then there.
## Micromamba and environment files
Under the hood, it uses
[Micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)
instead of Conda in order to speed up installations but it should not really
matter for the functionality.
The one place where I found it to matter is that you have to specify `channels`
in the environment file.
Instead of this (example taken from [conda
documentation](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually)):
```yaml
name: stats
dependencies:
- numpy
- pandas
```
You need to do this:
```yaml
name: stats
channels:
- defaults
dependencies:
- numpy
- pandas
```
But I believe that specifying channels explicitly is anyway good practice.
## Running on a supercomputer/cluster
On a cluster you might need to bind folders like here:
```
$ env APPTAINER_BIND="/cluster" ./conda.sif python
```
---
To build the image, I have used [this wonderful
guide](https://github.com/singularityhub/singularity-deploy) as starting point
and inspiration.