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Allow optional use of docker image ENTRYPOINT #253

@TedBrookings

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@TedBrookings

Currently dxCompiler clobbers the ENTRYPOINT of any docker image, because it uses the wdlTools dockerRunScript.ssp which sets the docker run argument --entrypoint /bin/bash \\. While this is fine for most workflows, it prevents a few workflows, or makes them much more verbose, and prevents some quality-of-life improvements in the image itself.

If this was changed to a template argument with default /bin/bash, e.g.

<%@ val entrypoint: String = "/bin/bash" %>

and then

# run as in the original configuration
docker run \\
-a stdout -a stderr \\
--memory=${maxMemory.toString} \\
--cidfile ${containerIdFile} \\
${bashDollar}{extraFlags} \\
--entrypoint "${entrypoint}" \\
-v ${hostRootDir}:${containerRootDir} \\
${imageName} ${commandFile}

This would (with additional Optional arguments in wdlTools and command line args in dxCompiler) allow users to specify their own entrypoint if desired.

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