update readme file with new docker instructions

This has to be included:

docker run -it -v$(pwd):/automap gitlab.lcsb.uni.lu:4567/minerva/automap /bin/bash assemble.sh

To check the result:

curl 'https://minerva-service.lcsb.uni.lu/minerva/api/convert/image/CellDesigner_SBML:pdf' -X POST \
    -T ./06-minerva_map_unp.xml \
    -H 'Content-Type: application/octet-stream' > out.pdf