gnasello/scintegration-env repository overview

⁠Standard use

To use this container after pulling you have to run the following command (you might need sudo privileges):

docker run -it --rm -p 7777:7777 -p 7878:7878 \
                     --volume $HOME:/home/host_home \
                     --workdir /home/host_home \
                     --entrypoint /usr/bin/bash \
                     --user root \
                     gnasello/scintegration-env:latest

Command shortcut to start jupyter lab (default port 7777) inside the container:

jl

You can change the port with the -p argument (e.g. jl -p 8888).

Command shortcut to start RStudio Server inside the container:

rs

To login in RStudio server use the following credentials:

username: rstudio password: rstudio

You will create new files and directories as root. Thus, if you want to allow any further user to access everything you created in the current directory, type the following command:

chmod -R 777 ./ 

⁠List of packages

Docker container built on gabnasello/datascience-env⁠

It installs the conda environment scib-pipeline-R4.0 created with scib-pipeline⁠

It adds the following packages to the conda environment

channels:
 - conda-forge
 - bioconda
dependencies:
 - ipywidgets
 - fa2
 - pyensembl

⁠Dockerfile

You find instructions to build this Docker Image in this GitHub page⁠.