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dabble-of-devops-bioanalyze/bioanalyze-docker-images: Docker Images for Jupyterhub + Bioinformatics

 October 15, 2021

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:

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

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