gnasello/spheroid-env repository overview

⁠Standard use

Run the following command (might need sudo priviledges):

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/spheroid-env:latest

Command shortcut to start jupyter lab inside the container:

jl

Command shortcut to start RStudio Server inside the container:

rs

To login in RStudio server use the following credentials:

username: rstudio password: rstudio

CellProfiler command:

/opt/conda/envs/cprofiler/bin/cellprofiler 

Ilastik command:

/ilastik/ilastik-1.3.3post3-Linux/run_ilastik.sh

ImageJ/Fiji command:

/imagej/Fiji.app/ImageJ-linux64

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

• Conda environment added:

- cprofiler from CellProfiler⁠

• Ilastik⁠ software

• Fiji⁠ software

⁠Dockerfile

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