[ARVADOS] updated: 64b24877bdb4b35938e8b691463b78073a4fd31d

[git at public.curoverse.com]

Summary of changes:
 .../controllers/pipeline_instances_controller.rb   |    6 ++
 apps/workbench/app/helpers/provenance_helper.rb    |   68 +++++++------------
 apps/workbench/app/models/collection.rb            |    7 ++
 .../pipeline_instances/_show_components.html.erb   |   10 ++--
 apps/workbench/test/unit/collection_test.rb        |   15 ++++-
 .../pipeline_templates/gatk-exome-fq-snp.json      |   21 ++++--
 doc/sdk/cli/index.html.textile.liquid              |    1 -
 .../tutorial-firstscript.html.textile.liquid       |    6 +-
 .../tutorial-new-pipeline.html.textile.liquid      |    8 ++-
 sdk/cli/arvados-cli.gemspec                        |    1 +
 sdk/cli/bin/arv-run-pipeline-instance              |   55 ++++++++++++++--
 sdk/cli/bin/crunch-job                             |   12 +++-
 .../app/controllers/arvados/v1/jobs_controller.rb  |    8 +-
 .../app/controllers/arvados/v1/users_controller.rb |    4 +-
 services/api/app/models/job.rb                     |    1 +
 services/api/app/models/user.rb                    |   16 ++--
 ...140324024606_add_output_is_persistent_to_job.rb |    5 ++
 services/api/db/schema.rb                          |    7 +-
 services/api/script/setup-new-user.rb              |    6 +-
 .../functional/arvados/v1/jobs_controller_test.rb  |    2 +
 .../functional/arvados/v1/users_controller_test.rb |   48 +++++++-------
 services/api/test/unit/user_test.rb                |   30 ++++----
 22 files changed, 208 insertions(+), 129 deletions(-)
 create mode 100644 services/api/db/migrate/20140324024606_add_output_is_persistent_to_job.rb

       via  64b24877bdb4b35938e8b691463b78073a4fd31d (commit)
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       via  6232434d6b86192b0531bacd7e4f0d5ae589f368 (commit)
       via  b0af0440838407be80c6208b15f969bc2942008e (commit)
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       via  9a405be1112c8bad4c56160a4fc234943449f7c5 (commit)
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       via  381f3ce2529a027cc0eb1c402b94135711658f6b (commit)
       via  6a8e3decba6bf4cd890bf98241646d0d070990b7 (commit)
       via  73e9bb7585add05c044a80c6811681d58b6148b4 (commit)
       via  69d0e98d74c221ba2161b4851c51dd47ee7a9409 (commit)
      from  c6043720763ecad450078728e2a3c815c51148bc (commit)

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commit 64b24877bdb4b35938e8b691463b78073a4fd31d
Merge: c604372 e661ffb
Author: Tom Clegg <tom at curoverse.com>
Date:   Fri Mar 28 15:21:03 2014 -0400

    Merge branch '1932-job-output-persistent'
    
    closes #1932


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