I am pretty new to Fiji and usage of it, so I wanted to ask on how I can utilise it in Gitlab CI/CD.
I use a cython file, in which I initialize Fiji. This I convert to a C file, and then use GCC to convert to an executable in the pipeline. Further, I try to run the executable in the pipeline, and it gives me all sorts of errors.
I get Fiji by
curl -L https://downloads.imagej.net/fiji/latest/fiji-linux64.zip -o fiji-linux64.zip
When I use python image for the job, I get error of not finding maven for running the imagej.init() line. I am unsure how to include maven into the job. I am unable to use apt-get install maven, as it shows unable to locate package.
When I use maven image for the job, I get error of error while loading shared libraries: libpython3.9.so.1.0, therefore saying it needs python image. Even if I use apt-get install python, does not work.
I have been stuck on this for quite sometime, and will be happy to answer any doubts related to this. Thanks in advance.