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https://github.com/geertvangeest/scs-docker
Dockerfiles for images hosted at https://hub.docker.com/r/geertvangeest/single_cell_summerschool
https://github.com/geertvangeest/scs-docker
containers deep-learning jupyter jupyter-notebook
Last synced: 11 days ago
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Dockerfiles for images hosted at https://hub.docker.com/r/geertvangeest/single_cell_summerschool
- Host: GitHub
- URL: https://github.com/geertvangeest/scs-docker
- Owner: GeertvanGeest
- Created: 2021-08-23T08:16:29.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-09-03T07:26:39.000Z (over 3 years ago)
- Last Synced: 2024-12-05T11:18:23.863Z (2 months ago)
- Topics: containers, deep-learning, jupyter, jupyter-notebook
- Language: Dockerfile
- Homepage:
- Size: 22.5 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## The containers
The following tags are in the docker hub repository at:
[https://hub.docker.com/r/geertvangeest/single_cell_summerschool](https://hub.docker.com/r/geertvangeest/single_cell_summerschool):
- `general-jupyter`: jupyter notebook container for general exercises in python (using scanpy). It also includes the conda environment for the multi-omics exercises (sc2021-multiomics-environment). Simply change the kernel in the python notebook to use the environment.
- `general-rstudio`: rstudio server container for the general exercsies in R.
- `dgn-rstudio`: rstudio server container for deep learning exercises with access to a gpu
- `dgn-jupyter`: jupyter notebook container for deep learning exercsies with access to a gpu
For the dockerfiles and other documentation visit:
[https://github.com/GeertvanGeest/scs-docker/](https://github.com/GeertvanGeest/scs-docker/)
### Running a jupyter notebook container locally
```sh
docker run --rm -v $PWD:/home/jovyan -p 8888:8888 geertvangeest/single_cell_summerschool:general-jupyter
```
Use the link that is provided in your console to go to the notebook in your browser.
Change `$PWD` to any other directory if you do not want to mount your current directory.
### Running an Rstudio container locally
```sh
docker run --rm -v $PWD:/home/rstudio -p 8787:8787 -e PASSWORD=yourpasswordhere geertvangeest/single_cell_summerschool:general-rstudio
```
If it is running successfully rstudio server is available at `http://localhost:8787`.
Your username is **rstudio** and the password is provided by the environment variable PASSWORD (i.e. *yourpasswordhere* in the example).
Change `$PWD` to any other directory if you do not want to mount your current directory.