Fix to properly run the command within the docker instance. #39
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Not all the docker images have to have
/bin/sh
shell,and the command line itself is obtained from the received TES request.
So, instead of writing the command to a shell script, and running the shell script within the container instance, the patch makes docker running the command within the container instance.
If this patch is accepted, some janitorial work would be needed, as all the script generation and permissions setting machinery could be removed.
Also, a similar change should be applied for the scenarios where singularity is being used instead of docker