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Add CannoliCommand and CannoliAlignerCommand. #54

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heuermh commented Jul 5, 2017

Adding CannoliCommand and CannoliAlignerCommand, work in progress towards #34. I get a little shaky with the Scala companion stuff, let me know if this looks like the right approach.

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AmplabJenkins commented Jul 5, 2017

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/42/

Build result: FAILURE

[...truncated 15 lines...] > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/54/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 49c7e9e # timeout=10Checking out Revision 49c7e9e (origin/pr/54/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 49c7e9e3ba2367d63a3171e7b6385b7014fd48bdFirst time build. Skipping changelog.Triggering cannoli-prb ? 2.6.0,2.11,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.11,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.6.0,2.10,1.6.1,centosTriggering cannoli-prb ? 2.3.0,2.10,2.0.0,centosTriggering cannoli-prb ? 2.3.0,2.11,1.6.1,centosTriggering cannoli-prb ? 2.6.0,2.11,2.0.0,centosTriggering cannoli-prb ? 2.3.0,2.10,1.6.1,centoscannoli-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.11,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.10,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.10,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.11,1.6.1,centos completed with result FAILUREcannoli-prb ? 2.6.0,2.11,2.0.0,centos completed with result FAILUREcannoli-prb ? 2.3.0,2.10,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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coveralls commented Jul 6, 2017

Coverage Status

Coverage decreased (-2.6%) to 32.66% when pulling 2fb7fe4 on heuermh:cannoli-command into 7a098f6 on bigdatagenomics:master.

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AmplabJenkins commented Jul 6, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/43/
Test PASSed.

@fnothaft

Pretty sure this is just a WIP ;)

optionalExtensions: Seq[String]): Seq[String] = {
// oddly, the hadoop fs apis don't seem to have a way to do this?
def canonicalizePath(fs: FileSystem, path: Path): String = {

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@heuermh

heuermh Oct 27, 2017

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idk, you wrote that comment :)

}
abstract class CannoliCommand[A <: CannoliArgs] extends BDGSparkCommand[A] with Logging {
// todo: various docker stuff

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@fnothaft

fnothaft Jul 7, 2017

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Just flagging this as a TODO.

pathsWithScheme ++ optionalPathsWithScheme
}
// todo: various index stuff

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fnothaft Jul 7, 2017

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Just flagging this as a TODO as well.

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heuermh commented Jul 7, 2017

Pretty sure this is just a WIP ;)

Yup, looking for feedback on whether these abstract classes might be the right approach.

@heuermh heuermh modified the milestone: 0.2.0 Jul 26, 2017

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heuermh commented Jan 24, 2018

Closing in favor of approach in #69.

@heuermh heuermh closed this Jan 24, 2018

@heuermh heuermh deleted the heuermh:cannoli-command branch Jan 24, 2018

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