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Building Singularity image with CellProfiler 4

Note: At the time of writing this, the working version of CellProfiler was 4.2.1

Build singularity image

Bulding the singularity image

  • Build the singularity image with
sudo singularity build cellprofiler4.sif cp4_ubuntu20.def

Sandbox version

Building the sandbox

  • Build a sandbox version from .def file
sudo singularity build --sandbox cellprofiler4 cp4_ubuntu20.def

Installing required packages inside the sandbox

  • Enter the sandbox with
sudo singularity shell --writable cellprofiler4
  • Install necessary packages into the sandbox
apt-get install -y package_name
  • Exit the singularity shell mode with
exit

Fix sandbox to a singularity image

sudo singularity build cellprofiler4.sif cellprofiler4

Run CellProfiler

  • Enter singularity container with
singularity shell cellprofiler4.sif
  • Inside the singularity shell, check CellProfiler version with
cellprofiler --version
  • Run CellProfiler with
cellprofiler

Running CellProfiler as native app

  • Create two directories
mkdir libexec bin
  • Pull the singularity image with
singularity pull --arch amd64 libexec/cellprofiler4.sif library://pranjaldhole/cv/cellprofiler4:latest

You can find the image on singularity hub here.

  • Create an executable and make it executable and put it in the same folder as .sif file:
cat >libexec/cellprofiler.sh<<"EOF"
#!/bin/bash
export SINGULARITY_BINDPATH="$HOME/fileservers/chd"
dir="$(dirname $(readlink -f ${BASH_SOURCE[0]}))"
img="cellprofiler4.sif"
cmd=$(basename "$0")
arg="$@"
singularity exec "${dir}/${img}" $cmd $arg
EOF

chmod 755 libexec/cellprofiler.sh
  • Create symlinks in bin directory for apps within image you want to run
ln -s ../libexec/cellprofiler.sh bin/cellprofiler
  • Here is how the directory structure should look like
.
├── bin
│   └── cellprofiler -> ../libexec/cellprofiler.sh
└── libexec
    ├── cellprofiler4.sif
    └── cellprofiler.sh
  • Add the following line to your .bashrc and source the .bashrc file or open a new terminal. Change the path to appropriate bin directory.
export PATH=$PATH:$HOME/path_to_repo/cellprofiler/bin
  • Test the location of the app with
$ which cellprofiler
> export /home/user/path_to_cellprofiler_dir/bin/cellprofiler
  • Now you can run cellprofiler from the image as if its native app. Test CellProfiler with
$ cellprofiler --version
> 4.2.1

or run CellProfiler with

cellprofiler