[ARVADOS] updated: 0042e4b42d9f4d3900aefc68617cb28c5a61a522

[git at public.curoverse.com]

Summary of changes:
 .../controllers/pipeline_instances_controller.rb   |  6 ---
 .../app/helpers/pipeline_components_helper.rb      |  3 +-
 .../app/helpers/pipeline_instances_helper.rb       |  1 +
 apps/workbench/app/helpers/provenance_helper.rb    |  5 --
 apps/workbench/app/models/pipeline_instance.rb     | 14 ++++++
 .../views/application/_job_status_label.html.erb   |  4 +-
 .../collections/_show_source_summary.html.erb      |  9 ++--
 .../workbench/app/views/jobs/_show_status.html.erb |  4 +-
 .../_show_components_running.html.erb              | 12 +++--
 .../schema/PipelineTemplate.html.textile.liquid    | 10 +++-
 .../pipeline_templates/gatk-exome-fq-snp.json      | 14 +++---
 .../running-external-program.html.textile.liquid   |  1 -
 .../tutorial-submit-job.html.textile.liquid        |  1 -
 sdk/cli/bin/arv-run-pipeline-instance              | 58 ++++++++++------------
 sdk/cli/bin/crunch-job                             | 26 +---------
 services/api/Gemfile                               |  2 +-
 services/api/Gemfile.lock                          |  6 +--
 services/api/app/models/job.rb                     |  1 -
 ...826180337_remove_output_is_persistent_column.rb |  9 ++++
 services/api/db/structure.sql                      |  5 +-
 20 files changed, 96 insertions(+), 95 deletions(-)
 create mode 100644 services/api/db/migrate/20140826180337_remove_output_is_persistent_column.rb

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commit 0042e4b42d9f4d3900aefc68617cb28c5a61a522
Merge: 3204b60 3630931
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Aug 27 17:04:24 2014 -0400

    Merge branch '3342-pipeline-output-current-project' closes #3342


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