title: docker: executable file not found in $PATH solution without changing CMD
body: <p>I am trying to run the official bwa docker <a href="https://hub.docker.com/r/biocontainers/bwa/" rel="nofollow noreferrer">https://hub.docker.com/r/biocontainers/bwa/</a>, and I keep getting an error:</p>
  
  <pre><code>sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa "index /opt/inputs/hg19.fa"
  docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index /opt/inputs/hg19.fa\": stat index /opt/inputs/hg19.fa: no such file or directory": unknown.
  ERRO[0000] error waiting for container: context canceled 
  </code></pre>
  
  <p>EDIT: Removing the double quotes from the lst string gives a different error:</p>
  
  <pre><code>sudo docker run -u="root" -v ~/files/:/opt/inputs/ biocontainers/bwa index /opt/inputs/hg19.fa
  docker: Error response from daemon: OCI runtime create failed: container_linux.go:348: starting container process caused "exec: \"index\": executable file not found in $PATH": unknown.
  </code></pre>
  
  <p>I have found the reason behind it here:</p>
  
  <p><a href="https://stackoverflow.com/questions/27158840/docker-executable-file-not-found-in-path">docker: executable file not found in $PATH</a></p>
  
  <p>This is the correct reason, but since this file was pre-build, and I want to use the official release, I cannot change the CMD synthax in Dockerfile. How can I make this work without changing the container itself?</p>