These docker images are built to use as a part of a full stack Bioinformatics Analysis Environment. Each image can be used on it's own or as a part of a Jupyterhub Cluster.
Each image is meant to be a full fledged ecosystem for Bioinformatics. Images:
- Are fully ready to use with a Jupyterhub or Dask Gateway Cluster.
- RStudio installed
- Jupyterlab installed
- Common software packages for data science such as Pandas, SciKit Learn, and TidyVerse
- Bioinformatics workflow runners: Snakemake and Nextflow.
- Workflow Orchestration systems: Prefect and Airflow.
- Use the excellent Pangeo Project as a base.
- Documentation packages such as Jupyterbook and RBookdown.
See each of the images at Dockerhub.
Please note that this project is still under rapid development and the system used for tagging is likely to change.
Cellprofiler Free open-source software for measuring and analyzing cell images.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| cellprofiler | 4.1.3 | dabbleofdevops/cellprofiler:cellprofiler-4.1.3--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| cellprofiler | 4.0.1 | dabbleofdevops/cellprofiler:cellprofiler-4.0.1--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| cellprofiler | 4.1.3 | dabbleofdevops/cellprofiler:cellprofiler-4.1.3--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| cellprofiler | 4.0.1 | dabbleofdevops/cellprofiler:cellprofiler-4.0.1--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| cellprofiler | 4.1.3 | dabbleofdevops/cellprofiler:cellprofiler-4.1.3--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| cellprofiler | 4.0.1 | dabbleofdevops/cellprofiler:cellprofiler-4.0.1--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
R R is a free software environment for statistical computing and graphics.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| conda_r | 4.0.3 | dabbleofdevops/conda_r:conda_r-4.0.3--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| conda_r | 3.6.1 | dabbleofdevops/conda_r:conda_r-3.6.1--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| conda_r | 4.0.3 | dabbleofdevops/conda_r:conda_r-4.0.3--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| conda_r | 3.6.1 | dabbleofdevops/conda_r:conda_r-3.6.1--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| conda_r | 4.0.3 | dabbleofdevops/conda_r:conda_r-4.0.3--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| conda_r | 3.6.1 | dabbleofdevops/conda_r:conda_r-3.6.1--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
Scanpy Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| scanpy | 1.6.0 | dabbleofdevops/scanpy:scanpy-1.6.0--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| scanpy | 1.6.0 | dabbleofdevops/scanpy:scanpy-1.6.0--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| scanpy | 1.6.0 | dabbleofdevops/scanpy:scanpy-1.6.0--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
Napari multi-dimensional image viewer for python.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| napari | 0.4.2 | dabbleofdevops/napari:napari-0.4.2--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| napari | 0.4.2 | dabbleofdevops/napari:napari-0.4.2--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| napari | 0.4.2 | dabbleofdevops/napari:napari-0.4.2--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
Seurat R Toolkit for single cell genomics.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| seurat | 4.0.0 | dabbleofdevops/seurat:seurat-4.0.0--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| seurat | 4.0.0 | dabbleofdevops/seurat:seurat-4.0.0--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| seurat | 4.0.0 | dabbleofdevops/seurat:seurat-4.0.0--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
The ML image hosts many different ML packages.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| ml | 1.0.0 | dabbleofdevops/ml:ml-1.0.0--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| ml | 1.0.0 | dabbleofdevops/ml:ml-1.0.0--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| ml | 1.0.0 | dabbleofdevops/ml:ml-1.0.0--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
The STEM Away ML image was build in collaboration with STEMAway for the Summer 2021 internship.
| name | version | docker_image | pangeo_version | python_version | snakemake_version | nextflow_version | prefect_version | airflow_version |
|---|---|---|---|---|---|---|---|---|
| stem_away_ml | 1.0.0 | dabbleofdevops/stem_away_ml:stem_away_ml-1.0.0--pangeo-2021.08.17--python-3.8 | 2021.08.17 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| stem_away_ml | 1.0.0 | dabbleofdevops/stem_away_ml:stem_away_ml-1.0.0--pangeo-2021.06.05--python-3.8 | 2021.06.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
| stem_away_ml | 1.0.0 | dabbleofdevops/stem_away_ml:stem_away_ml-1.0.0--pangeo-2021.04.05--python-3.8 | 2021.04.05 | 3.8* | 6.7.0 | 21.04.0 | 0.15.4 | 2.1.4 |
(This information is completely grabbed from Pangeo)
If deploying in a Jupyterhub on Kubernetes cluster you'll need to make sure you're using the same pangeo versions.
| dask-gateway | Pangeo Version tag |
|---|---|
| 0.9 | 2020.11.06 |
| 0.8 | 2020.07.28 |
| 0.7 | 2020.04.22 |