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Support loading reference files from HDFS/other file system #50

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fnothaft opened this issue Jul 3, 2017 · 2 comments
Closed

Support loading reference files from HDFS/other file system #50

fnothaft opened this issue Jul 3, 2017 · 2 comments
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@fnothaft
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@fnothaft fnothaft commented Jul 3, 2017

This is supported as part of the ADAM pipe transform using the optional files parameter, which copies files from a "global" path into local temp space on each Spark executor.

@fnothaft fnothaft added the enhancement label Jul 3, 2017
@fnothaft fnothaft added this to the 0.1.0 milestone Jul 3, 2017
@heuermh heuermh modified the milestones: 0.1.0, 0.2.0 Jan 24, 2018
@heuermh
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@heuermh heuermh commented Feb 14, 2018

So what needs to be done for this issue? The files parameter in the pipe API is available for every Cannoli cli class to call, do we simply need to add a command line argument flag to add reference file(s) to files? Such already exists in https://github.com/bigdatagenomics/cannoli/blob/master/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bwa.scala#L91

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@heuermh heuermh commented Mar 22, 2018

Fixed by #107.

@heuermh heuermh closed this Mar 22, 2018
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