Add a 'distribution' module to create assemblies

[massie]

o Moves the maven-assembly-plugin from adam-cli to the
new distribution module
o Updates the adam-submit and friends to work from source
or binary distributions
o Generates docs and adds them to the distribution
o Adds LICENSE, NOTICE.txt, CHANGES.md, etc to distribution

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 888f32e automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 8741a95 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 8741a95 > git rev-list 1be1bb20981fa59633c192368558628806496153 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[fnothaft]

+1, but looks like you need pandoc on Jenkins.

[fnothaft]

Also, not sure if this is just Github's source browser showing things incorrectly or not, but in addition to adding distribution/src/main/assembly/assembly.xml, shouldn't you remove adam-cli/src/main/assembly/assembly.xml. If this is removed on your end, ignore me.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 4ae1949 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 9c15ef40777b94d6598b258d478db7d134b25270 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 9c15ef40777b94d6598b258d478db7d134b25270 > git rev-list 1be1bb20981fa59633c192368558628806496153 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[AmplabJenkins]

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Build result: FAILURE

GitHub pull request #509 of commit 90239ed automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 > git rev-list 050a31c # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 90239ed automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 > git rev-list 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

@fnothaft Good catch on removing the adam-cli assemblies.xml file.

I tried to install pandoc on the workers but realized that it wasn't going to be easy to maintain (there were some latex modules that I would have had to track down). Instead, for now, I've setup the build script to exit with a warning if pandoc isn't found. It's not ideal but at least we can get a release out.

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Build result: FAILURE

GitHub pull request #509 of commit 45155de automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision b4c55a2fab3e0c725bb0956b5a34b87527742535 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b4c55a2fab3e0c725bb0956b5a34b87527742535 > git rev-list 2eb1b62ebcf7374c97e43184234ce6e340f00fe0 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

[massie]

I just realized that I always say please to Jenkins when I don't really need to.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 45155de automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision b4c55a2fab3e0c725bb0956b5a34b87527742535 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b4c55a2fab3e0c725bb0956b5a34b87527742535 > git rev-list b4c55a2fab3e0c725bb0956b5a34b87527742535 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[fnothaft]

@massie it looks like you need to say "please" for test/retest. Only "add to whitelist" is more perfunctory ;)

[fnothaft]

scripts/format-sources :-P

[massie]

The issue is that the repo is left dirty. I'm investigating now.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 45155de automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision b4c55a2fab3e0c725bb0956b5a34b87527742535 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b4c55a2fab3e0c725bb0956b5a34b87527742535 > git rev-list b4c55a2fab3e0c725bb0956b5a34b87527742535 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #509 of commit 45155de automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision b4c55a2fab3e0c725bb0956b5a34b87527742535 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b4c55a2fab3e0c725bb0956b5a34b87527742535 > git rev-list b4c55a2fab3e0c725bb0956b5a34b87527742535 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 45155de automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prbCloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision b4c55a2fab3e0c725bb0956b5a34b87527742535 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f b4c55a2fab3e0c725bb0956b5a34b87527742535 > git rev-list b4c55a2fab3e0c725bb0956b5a34b87527742535 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins test this please.

[massie]

Jenkins test this please.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 2c017bd automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 361e45d588b4ffa993216641e92ced94758f4fbb (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 361e45d588b4ffa993216641e92ced94758f4fbb > git rev-list b4c55a2fab3e0c725bb0956b5a34b87527742535 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

[AmplabJenkins]

Test FAILed.
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Build result: FAILURE

GitHub pull request #509 of commit 9b3a2c4 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/509/merge^{commit} # timeout=10Checking out Revision 455fc91f98227fc8588bc6687695a910ae30d36c (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 455fc91f98227fc8588bc6687695a910ae30d36c > git rev-list 361e45d588b4ffa993216641e92ced94758f4fbb # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 2.2.0,centosTriggering ADAM-prb » 1.0.4,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILURE
Test FAILed.

[massie]

Jenkins, test this please.

... and make it work this time!

[massie]

Jenkins, test this please.

[AmplabJenkins]

Test PASSed.
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Test PASSed.

[massie]

Yes!

@fnothaft Look good to you?

[fnothaft]

Looks great @massie! Thank you, and merged!