Not the OP, but replying to offer a suggestion in this respect.
I'll often do something similar to this, where I have a CLI tool that I'm not ready to deploy server-wide yet, and has hefty dependencies.
The pattern I use is to have a wrapper shell script that calls:
docker run -it --rm --volume "$(pwd)/$1:/file_to_process:z" --user $(id -u) container-image /opt/command_to_run /fileToProcess
This runs "/opt/command_to_run /fileToProcess" inside a container as the current uid, mounting the parameter to the shell script as "/file_to_process" inside the container.
The :z mount parameter may or may not be needed depending upon whether you have SELinux enabled or not (by default, SELinux prevents countainers accessing any file on the host, and :z changes the SE context to allow access). I don't know if this is the case with EL6 tho.
The -t parameter shouldn't be used if your script is running in a pipeline (it creates a pseudo-tty). So it may be worth having some kind of conditional to remove this.
The wrapper I use also has a conditional to add the "$(pwd)" prefix to the call parameter only if the parameter is a relative path.