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Factor out docker/mapping code #34

fnothaft opened this Issue May 3, 2017 · 2 comments


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fnothaft commented May 3, 2017

In #25 we add the ability to run BWA through Docker, and to mount reference files locally on the executors. We should factor this code out from BWA into a general pattern that we can use across all of the tools in cannoli.

It should support the matrix of:

  • Running tools natively or running tools from a docker container
  • Mounting index files local to the executor, mounting index files into the docker container, or not doing anything (i.e., index/ref files are on a globally mounted file system)

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heuermh commented Oct 27, 2017

@fnothaft is git head the latest you've been using for BWA in cannoli? I need to better grok what is going on with all the path munging so that I can flesh out pull request #54.


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heuermh commented Mar 22, 2018

Fixed by #107.

@heuermh heuermh closed this Mar 22, 2018

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