BioAnalyze Docker Images

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.

Bioinformatics Ecosystem

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.

Base Image: R: 4.0.3 RStudio: 1.2.5042 Conda: 4.9.2-0

cellprofiler

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

conda_r

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 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

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

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

ml

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

stem_away_ml

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

Dask-gateway compatibility

(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