ImageJ BaSiC shading correction for use with Ashlar

Create a container:

docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash

where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container.

Once inside the container, do ls /data to ensure your data is there, followed by

ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
  "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"

for each input.ome.tiff in your data directory.

Galaxy's default job configuration for local Docker execution does not deal with ENTRYPOINTs properly; please ensure you have the following line in your job configuration file's local Docker <destination> block:

<param id="docker_run_extra_arguments">&#45;&#45;entrypoint ""</param>

This parameter (--entrypoint "") nullifies the ENTRYPOINT, allowing the CMD to be overwritten by Galaxy, and Galaxy's generated tool_script.sh to be executed as expected.