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Description
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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