[ARVADOS] updated: d28b1cebc8b799ea1e65a50826602392b446ea29

git at public.curoverse.com git at public.curoverse.com
Mon Jul 7 12:47:57 EDT 2014


Summary of changes:
 .../_show_advanced_cli_example.html.erb            |   4 +
 .../_show_advanced_curl_example.html.erb           |   1 +
 .../_show_advanced_python_example.html.erb         |   1 +
 .../app/views/projects/_index_projects.html.erb    |  11 +-
 crunch_scripts/arvados-bcbio-nextgen.py            | 135 ++++++++++++++++++
 crunch_scripts/run-command                         |  43 ++++--
 doc/Rakefile                                       |   2 +-
 doc/_config.yml                                    |   5 +-
 doc/_includes/_alert_docker.liquid                 |   4 +
 doc/api/methods/jobs.html.textile.liquid           |  20 +++
 doc/install/index.html.textile.liquid              |  18 ++-
 doc/install/install-docker.html.textile.liquid     | 157 +++++++++++++++++++++
 .../running-external-program.html.textile.liquid   |   2 +-
 .../tutorial-firstscript.html.textile.liquid       |   2 +-
 .../tutorial-new-pipeline.html.textile.liquid      |   2 +-
 docker/bcbio-nextgen/Dockerfile                    |  47 ++++++
 docker/build_tools/Makefile                        |  16 ++-
 .../{bwa-samtools => java-bwa-samtools}/Dockerfile |   3 +-
 docker/jobs/Dockerfile                             |   6 +-
 docker/mkimage-debootstrap.sh                      |   2 +
 sdk/cli/arvados-cli.gemspec                        |   1 +
 sdk/cli/bin/arv-run-pipeline-instance              |  16 +--
 sdk/cli/bin/crunch-job                             |  25 ++--
 sdk/python/bin/arv-ls                              |   3 +-
 sdk/python/tests/test_arv_put.py                   |   5 +-
 sdk/ruby/arvados.gemspec                           |   1 +
 services/api/Gemfile                               |   2 +-
 services/api/Gemfile.lock                          |   8 +-
 .../app/controllers/arvados/v1/links_controller.rb |  26 ++++
 services/api/app/models/arvados_model.rb           |  19 +++
 services/api/app/models/blob.rb                    |   2 +-
 services/api/app/models/job.rb                     |  18 ++-
 services/api/app/models/link.rb                    |  36 ++---
 services/api/app/models/user.rb                    |  11 ++
 services/api/config/routes.rb                      |   1 +
 services/api/lib/load_param.rb                     |   6 +-
 services/api/script/crunch-dispatch.rb             |   2 +-
 .../arvados/v1/commits_controller_test.rb          |   4 +-
 .../api/test/functional/arvados/v1/git_setup.rb    |  27 ----
 .../arvados/v1/job_reuse_controller_test.rb        |   4 +-
 .../functional/arvados/v1/jobs_controller_test.rb  |   4 +-
 services/api/test/helpers/git_test_helper.rb       |  30 ++++
 .../api/test/integration/crunch_dispatch_test.rb   |   4 +-
 services/api/test/integration/permissions_test.rb  |  89 ++++++++++++
 .../test/integration/serialized_encoding_test.rb   |   4 +-
 services/api/test/integration/websocket_test.rb    |   2 +-
 services/api/test/unit/job_test.rb                 |  89 ++++++++----
 services/api/test/unit/link_test.rb                |   4 +
 services/api/test/unit/permission_test.rb          | 103 ++++++++++++++
 services/keep/src/keep/keep.go                     |   6 +-
 services/keep/src/keep/volume.go                   |   3 +-
 services/keep/src/keep/volume_unix.go              |   7 +-
 52 files changed, 889 insertions(+), 154 deletions(-)
 create mode 100755 crunch_scripts/arvados-bcbio-nextgen.py
 create mode 100644 doc/_includes/_alert_docker.liquid
 create mode 100644 doc/install/install-docker.html.textile.liquid
 create mode 100644 docker/bcbio-nextgen/Dockerfile
 rename docker/{bwa-samtools => java-bwa-samtools}/Dockerfile (90%)
 delete mode 100644 services/api/test/functional/arvados/v1/git_setup.rb
 create mode 100644 services/api/test/helpers/git_test_helper.rb

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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit d28b1cebc8b799ea1e65a50826602392b446ea29
Merge: b74393c c0cda7d
Author: radhika <radhika at curoverse.com>
Date:   Mon Jul 7 12:40:56 2014 -0400

    Merge branch 'master' into 3106-modal-loading-indicator


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