use raw github url of run.sh in marathon url
eg. { "id": "web", "cmd": "chmod +x run.sh && ./run.sh && cd testmarathonapp/app && python -m SimpleHTTPServer $PORT", "mem": 50, "cpus": 0.1, "instances": 1, "constraints": [ ["hostname", "UNIQUE"] ], "servicePorts": [8032], "uris": ["https://raw.githubusercontent.com/samek/testmarathonapp/master/run.sh"] }