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Adding wrapper for BCFtools norm. #71

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merged 1 commit into from
Jan 24, 2018
Merged

Adding wrapper for BCFtools norm. #71

merged 1 commit into from
Jan 24, 2018

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heuermh
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@heuermh heuermh commented Sep 13, 2017

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Test PASSed.
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fnothaft
fnothaft requested changes Oct 27, 2017
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cli/src/main/scala/org/bdgenomics/cannoli/cli/Bcftools.scala Outdated
val bcftoolsCommand = if (args.useDocker) {
Seq("docker",
"run",
"--rm",
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You'll need -it as well.

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There is no such option in the latest version of docker, I assume you mean --interactive?

$ docker --version
Docker version 17.09.0-ce, build afdb6d4

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Yes, sorry about that!

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heuermh commented Oct 27, 2017

With an additional --mount argument for the reference argument, this works for me locally using docker.

@heuermh heuermh added this to the 0.1.0 milestone Jan 24, 2018
@heuermh heuermh merged commit 6a705e5 into bigdatagenomics:master Jan 24, 2018
@heuermh heuermh deleted the bcftools branch January 24, 2018 17:57
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@heuermh @AmplabJenkins @fnothaft