scMultiFlow

This is the Docker image for Python and R bioinformatics tools. It contains:

• Python 3.12.4, Anaconda 2024-06.1, JupyterHub 5.1.0 (with R kernel)
• R 4.3.3, RStudio 2023.12.0, Bioconductor 3.18, libraries for single-cell analysis, including Seurat 5.1.0.
• cellranger 8.0.1, cellranger-arc-2.0.2 (see Dockerfile how to manually add it, because of EULA)
• scROCK and scMoMsQC libraries

Usage

docker pull bansalvi/scmultiflow
docker run --detach -p 18000:8000 -p 18787:8787 \
    --volume "$(realpath ..)/data":/data \
    --name scmultiflow-container bansalvi/scmultiflow

If using an old version of Ubuntu (below Ubuntu 22.04), to avoid errors use:

docker pull bansalvi/scmultiflow
docker run --detach -p 18000:8000 -p 18787:8787 \
    --volume "$(realpath ..)/data":/data \
    --name scmultiflow-container --security-opt seccomp=unconfined bansalvi/scmultiflow

You can access to JupyterHub by http://{docker-ip}:18000/

You can access to RStudio by http://{docker-ip}:18787/

One can change ports in Makefile used for Docker run.

Users

Both JupyterHub and RStudio use user list containing user1000, user1001, ..., user1009 by default, with password "1". It is done for compatibility with external volumes mounted into Docker, containing user notebooks and files. One can edit users.txt and rebuild Docker image with make build command if they want to change that.

Build

make build
make run