cd <path to pypesto base directory>/docker && docker build -t $USER/amici_pypesto:latest .

To install pyPESTO from a particular branch, e.g. develop, use the following line in the Dockerfile

RUN pip3 install git+https://github.com/ICB-DCM/pyPESTO.git@develop#egg=pypesto

environment file can be used with --set-env option of ch-run command. From charliecloud documentation:

" The purpose of --set-env=FILE is to set environment variables that cannot be inherited from the host shell, e.g. Dockerfile ENV directives or other build-time configuration "