[ARVADOS] updated: b54d7820e899733ce10b8960b1f04d0481f2e11f

git at public.curoverse.com git at public.curoverse.com
Tue Feb 11 09:23:15 EST 2014


Summary of changes:
 .gitignore                                         |    3 +-
 doc/Gemfile                                        |    4 +-
 doc/Gemfile.lock                                   |   63 ++---
 doc/README_FOR_APP                                 |    2 -
 doc/Rakefile                                       |   25 ++
 doc/_config.yml                                    |   96 +++++++-
 doc/_includes/{0-filter.py => _0_filter_py.liquid} |    0
 ...rt-incomplete.html => _alert-incomplete.liquid} |    0
 .../{alert-stub.html => _alert_stub.liquid}        |    0
 doc/_includes/_navbar_left.liquid                  |   20 ++
 .../{navbar_top.html => _navbar_top.liquid}        |    0
 .../{notebox-begin.html => _notebox_begin.liquid}  |    0
 .../{notebox-end.html => _notebox_end.liquid}      |    0
 ...h_script.py => _parallel_hash_script_py.liquid} |    0
 .../{run-md5sum.py => _run_md5sum_py.liquid}       |    0
 ...h_script.py => _tutorial_hash_script_py.liquid} |    0
 doc/_includes/navbar_left.html                     |   27 --
 doc/_layouts/default.html                          |  120 ---------
 doc/_layouts/default.html.liquid                   |  120 +++++++++
 doc/admin/cheat_sheet.html.textile.liquid          |   72 +++++
 doc/admin/cheat_sheet.textile                      |   73 ------
 doc/admin/index.html.md.liquid                     |   14 +
 doc/admin/index.md                                 |   15 -
 doc/api/authentication.html.textile.liquid         |   40 +++
 doc/api/authentication.textile                     |   40 ---
 doc/api/crunch-scripts.html.textile.liquid         |   46 ++++
 doc/api/crunch-scripts.textile                     |   46 ----
 doc/api/index.html.textile.liquid                  |   52 ++++
 doc/api/index.textile                              |   52 ----
 doc/api/methods.html.textile.liquid                |   80 ++++++
 doc/api/methods.textile                            |   80 ------
 .../api_client_authorizations.html.textile.liquid  |  109 ++++++++
 doc/api/methods/api_client_authorizations.textile  |  109 --------
 doc/api/methods/api_clients.html.textile.liquid    |   98 +++++++
 doc/api/methods/api_clients.textile                |   98 -------
 .../methods/authorized_keys.html.textile.liquid    |   98 +++++++
 doc/api/methods/authorized_keys.textile            |   98 -------
 doc/api/methods/collections.html.textile.liquid    |   98 +++++++
 doc/api/methods/collections.textile                |   98 -------
 doc/api/methods/groups.html.textile.liquid         |   98 +++++++
 doc/api/methods/groups.textile                     |   98 -------
 doc/api/methods/humans.html.textile.liquid         |   98 +++++++
 doc/api/methods/humans.textile                     |   98 -------
 doc/api/methods/job_tasks.html.textile.liquid      |   98 +++++++
 doc/api/methods/job_tasks.textile                  |   98 -------
 doc/api/methods/jobs.html.textile.liquid           |  130 ++++++++++
 doc/api/methods/jobs.textile                       |  130 ----------
 doc/api/methods/keep_disks.html.textile.liquid     |  114 ++++++++
 doc/api/methods/keep_disks.textile                 |  114 --------
 doc/api/methods/links.html.textile.liquid          |  109 ++++++++
 doc/api/methods/links.textile                      |  109 --------
 doc/api/methods/logs.html.textile.liquid           |   98 +++++++
 doc/api/methods/logs.textile                       |   98 -------
 doc/api/methods/nodes.html.textile.liquid          |  109 ++++++++
 doc/api/methods/nodes.textile                      |  109 --------
 .../methods/pipeline_instances.html.textile.liquid |   98 +++++++
 doc/api/methods/pipeline_instances.textile         |   98 -------
 .../methods/pipeline_templates.html.textile.liquid |   98 +++++++
 doc/api/methods/pipeline_templates.textile         |   98 -------
 doc/api/methods/repositories.html.textile.liquid   |  107 ++++++++
 doc/api/methods/repositories.textile               |  107 --------
 doc/api/methods/specimens.html.textile.liquid      |   98 +++++++
 doc/api/methods/specimens.textile                  |   98 -------
 doc/api/methods/traits.html.textile.liquid         |   98 +++++++
 doc/api/methods/traits.textile                     |   98 -------
 doc/api/methods/users.html.textile.liquid          |  126 +++++++++
 doc/api/methods/users.textile                      |  126 ---------
 .../methods/virtual_machines.html.textile.liquid   |  117 +++++++++
 doc/api/methods/virtual_machines.textile           |  117 ---------
 doc/api/permission-model.html.textile.liquid       |  107 ++++++++
 doc/api/permission-model.textile                   |  107 --------
 doc/api/resources.html.textile.liquid              |   49 ++++
 doc/api/resources.textile                          |   49 ----
 doc/api/schema/ApiClient.html.textile.liquid       |   38 +++
 doc/api/schema/ApiClient.textile                   |   38 ---
 .../ApiClientAuthorization.html.textile.liquid     |   44 ++++
 doc/api/schema/ApiClientAuthorization.textile      |   44 ----
 doc/api/schema/AuthorizedKey.html.textile.liquid   |   40 +++
 doc/api/schema/AuthorizedKey.textile               |   40 ---
 doc/api/schema/Collection.html.textile.liquid      |   45 ++++
 doc/api/schema/Collection.textile                  |   45 ----
 doc/api/schema/Commit.html.textile.liquid          |   38 +++
 doc/api/schema/Commit.textile                      |   38 ---
 doc/api/schema/CommitAncestor.html.textile.liquid  |   39 +++
 doc/api/schema/CommitAncestor.textile              |   39 ---
 doc/api/schema/Group.html.textile.liquid           |   37 +++
 doc/api/schema/Group.textile                       |   37 ---
 doc/api/schema/Human.html.textile.liquid           |   36 +++
 doc/api/schema/Human.textile                       |   36 ---
 doc/api/schema/Job.html.textile.liquid             |   83 ++++++
 doc/api/schema/Job.textile                         |   83 ------
 doc/api/schema/JobTask.html.textile.liquid         |   51 ++++
 doc/api/schema/JobTask.textile                     |   51 ----
 doc/api/schema/KeepDisk.html.textile.liquid        |   48 ++++
 doc/api/schema/KeepDisk.textile                    |   48 ----
 doc/api/schema/Link.html.textile.liquid            |   87 +++++++
 doc/api/schema/Link.textile                        |   87 -------
 doc/api/schema/Log.html.textile.liquid             |   39 +++
 doc/api/schema/Log.textile                         |   39 ---
 doc/api/schema/Node.html.textile.liquid            |   42 +++
 doc/api/schema/Node.textile                        |   42 ---
 .../schema/PipelineInstance.html.textile.liquid    |   41 +++
 doc/api/schema/PipelineInstance.textile            |   41 ---
 .../schema/PipelineTemplate.html.textile.liquid    |   37 +++
 doc/api/schema/PipelineTemplate.textile            |   37 ---
 doc/api/schema/Repository.html.textile.liquid      |   38 +++
 doc/api/schema/Repository.textile                  |   38 ---
 doc/api/schema/Specimen.html.textile.liquid        |   37 +++
 doc/api/schema/Specimen.textile                    |   37 ---
 doc/api/schema/Trait.html.textile.liquid           |   37 +++
 doc/api/schema/Trait.textile                       |   37 ---
 doc/api/schema/User.html.textile.liquid            |   43 +++
 doc/api/schema/User.textile                        |   43 ---
 doc/api/schema/VirtualMachine.html.textile.liquid  |   36 +++
 doc/api/schema/VirtualMachine.textile              |   36 ---
 doc/gen_api_method_docs.py                         |    1 -
 doc/index.html                                     |   46 ----
 doc/index.html.liquid                              |   47 ++++
 doc/install/client.html.textile.liquid             |   36 +++
 doc/install/client.textile                         |   36 ---
 .../create-standard-objects.html.textile.liquid    |   60 +++++
 doc/install/create-standard-objects.textile        |   60 -----
 doc/install/index.html.md.liquid                   |   17 ++
 doc/install/index.md                               |   18 --
 doc/install/install-api-server.html.md             |  114 ++++++++
 doc/install/install-api-server.md                  |  114 --------
 .../install-crunch-dispatch.html.textile.liquid    |  102 ++++++++
 doc/install/install-crunch-dispatch.textile        |  102 --------
 doc/install/install-workbench-app.html.md          |   63 +++++
 doc/install/install-workbench-app.md               |   63 -----
 doc/sdk/index.html.textile.liquid                  |   12 +
 doc/sdk/index.textile                              |   12 -
 .../crunch-utility-libraries.html.textile.liquid   |  225 ++++++++++++++++
 doc/sdk/python/crunch-utility-libraries.textile    |  225 ----------------
 doc/sdk/python/python.html.textile.liquid          |   10 +
 doc/sdk/python/python.textile                      |   10 -
 doc/sdk/python/sdk-python.html.textile.liquid      |  120 +++++++++
 doc/sdk/python/sdk-python.textile                  |  120 ---------
 .../examples/crunch-examples.html.textile.liquid   |   98 +++++++
 doc/user/examples/crunch-examples.textile          |   98 -------
 .../check-environment.html.textile.liquid          |   54 ++++
 doc/user/getting_started/check-environment.textile |   54 ----
 .../getting_started/community.html.textile.liquid  |   25 ++
 doc/user/getting_started/community.textile         |   25 --
 .../getting_started/ssh-access.html.textile.liquid |  217 ++++++++++++++++
 doc/user/getting_started/ssh-access.textile        |  217 ----------------
 .../getting_started/workbench.html.textile.liquid  |   18 ++
 doc/user/getting_started/workbench.textile         |   18 --
 doc/user/index.html.textile.liquid                 |   51 ++++
 doc/user/index.textile                             |   51 ----
 doc/user/reference/api-tokens.html.textile.liquid  |   47 ++++
 doc/user/reference/api-tokens.textile              |   47 ----
 doc/user/reference/sdk-cli.html.textile.liquid     |   81 ++++++
 doc/user/reference/sdk-cli.textile                 |   81 ------
 .../running-external-program.html.textile.liquid   |   67 +++++
 .../tutorials/running-external-program.textile     |   67 -----
 .../tutorial-firstscript.html.textile.liquid       |  124 +++++++++
 doc/user/tutorials/tutorial-firstscript.textile    |  124 ---------
 ...rial-gatk-variantfiltration.html.textile.liquid |  216 ++++++++++++++++
 .../tutorial-gatk-variantfiltration.textile        |  216 ----------------
 .../tutorial-job-debug.html.textile.liquid         |  156 +++++++++++
 doc/user/tutorials/tutorial-job-debug.textile      |  156 -----------
 .../tutorials/tutorial-job1.html.textile.liquid    |  233 +++++++++++++++++
 doc/user/tutorials/tutorial-job1.textile           |  233 -----------------
 .../tutorials/tutorial-keep.html.textile.liquid    |  136 ++++++++++
 doc/user/tutorials/tutorial-keep.textile           |  136 ----------
 .../tutorial-new-pipeline.html.textile.liquid      |  158 +++++++++++
 doc/user/tutorials/tutorial-new-pipeline.textile   |  158 -----------
 .../tutorial-parallel.html.textile.liquid          |   81 ++++++
 doc/user/tutorials/tutorial-parallel.textile       |   81 ------
 .../tutorial-trait-search.html.textile.liquid      |  273 ++++++++++++++++++++
 doc/user/tutorials/tutorial-trait-search.textile   |  273 --------------------
 doc/zenweb-liquid.rb                               |   41 +++
 doc/zenweb-textile.rb                              |   17 ++
 174 files changed, 6575 insertions(+), 6438 deletions(-)
 delete mode 100644 doc/README_FOR_APP
 create mode 100644 doc/Rakefile
 rename doc/_includes/{0-filter.py => _0_filter_py.liquid} (100%)
 rename doc/_includes/{alert-incomplete.html => _alert-incomplete.liquid} (100%)
 rename doc/_includes/{alert-stub.html => _alert_stub.liquid} (100%)
 create mode 100644 doc/_includes/_navbar_left.liquid
 rename doc/_includes/{navbar_top.html => _navbar_top.liquid} (100%)
 rename doc/_includes/{notebox-begin.html => _notebox_begin.liquid} (100%)
 rename doc/_includes/{notebox-end.html => _notebox_end.liquid} (100%)
 rename doc/_includes/{parallel_hash_script.py => _parallel_hash_script_py.liquid} (100%)
 rename doc/_includes/{run-md5sum.py => _run_md5sum_py.liquid} (100%)
 rename doc/_includes/{tutorial_hash_script.py => _tutorial_hash_script_py.liquid} (100%)
 delete mode 100644 doc/_includes/navbar_left.html
 delete mode 100644 doc/_layouts/default.html
 create mode 100644 doc/_layouts/default.html.liquid
 create mode 100644 doc/admin/cheat_sheet.html.textile.liquid
 delete mode 100644 doc/admin/cheat_sheet.textile
 create mode 100644 doc/admin/index.html.md.liquid
 delete mode 100644 doc/admin/index.md
 create mode 100644 doc/api/authentication.html.textile.liquid
 delete mode 100644 doc/api/authentication.textile
 create mode 100644 doc/api/crunch-scripts.html.textile.liquid
 delete mode 100644 doc/api/crunch-scripts.textile
 create mode 100644 doc/api/index.html.textile.liquid
 delete mode 100644 doc/api/index.textile
 create mode 100644 doc/api/methods.html.textile.liquid
 delete mode 100644 doc/api/methods.textile
 create mode 100644 doc/api/methods/api_client_authorizations.html.textile.liquid
 delete mode 100644 doc/api/methods/api_client_authorizations.textile
 create mode 100644 doc/api/methods/api_clients.html.textile.liquid
 delete mode 100644 doc/api/methods/api_clients.textile
 create mode 100644 doc/api/methods/authorized_keys.html.textile.liquid
 delete mode 100644 doc/api/methods/authorized_keys.textile
 create mode 100644 doc/api/methods/collections.html.textile.liquid
 delete mode 100644 doc/api/methods/collections.textile
 create mode 100644 doc/api/methods/groups.html.textile.liquid
 delete mode 100644 doc/api/methods/groups.textile
 create mode 100644 doc/api/methods/humans.html.textile.liquid
 delete mode 100644 doc/api/methods/humans.textile
 create mode 100644 doc/api/methods/job_tasks.html.textile.liquid
 delete mode 100644 doc/api/methods/job_tasks.textile
 create mode 100644 doc/api/methods/jobs.html.textile.liquid
 delete mode 100644 doc/api/methods/jobs.textile
 create mode 100644 doc/api/methods/keep_disks.html.textile.liquid
 delete mode 100644 doc/api/methods/keep_disks.textile
 create mode 100644 doc/api/methods/links.html.textile.liquid
 delete mode 100644 doc/api/methods/links.textile
 create mode 100644 doc/api/methods/logs.html.textile.liquid
 delete mode 100644 doc/api/methods/logs.textile
 create mode 100644 doc/api/methods/nodes.html.textile.liquid
 delete mode 100644 doc/api/methods/nodes.textile
 create mode 100644 doc/api/methods/pipeline_instances.html.textile.liquid
 delete mode 100644 doc/api/methods/pipeline_instances.textile
 create mode 100644 doc/api/methods/pipeline_templates.html.textile.liquid
 delete mode 100644 doc/api/methods/pipeline_templates.textile
 create mode 100644 doc/api/methods/repositories.html.textile.liquid
 delete mode 100644 doc/api/methods/repositories.textile
 create mode 100644 doc/api/methods/specimens.html.textile.liquid
 delete mode 100644 doc/api/methods/specimens.textile
 create mode 100644 doc/api/methods/traits.html.textile.liquid
 delete mode 100644 doc/api/methods/traits.textile
 create mode 100644 doc/api/methods/users.html.textile.liquid
 delete mode 100644 doc/api/methods/users.textile
 create mode 100644 doc/api/methods/virtual_machines.html.textile.liquid
 delete mode 100644 doc/api/methods/virtual_machines.textile
 create mode 100644 doc/api/permission-model.html.textile.liquid
 delete mode 100644 doc/api/permission-model.textile
 create mode 100644 doc/api/resources.html.textile.liquid
 delete mode 100644 doc/api/resources.textile
 create mode 100644 doc/api/schema/ApiClient.html.textile.liquid
 delete mode 100644 doc/api/schema/ApiClient.textile
 create mode 100644 doc/api/schema/ApiClientAuthorization.html.textile.liquid
 delete mode 100644 doc/api/schema/ApiClientAuthorization.textile
 create mode 100644 doc/api/schema/AuthorizedKey.html.textile.liquid
 delete mode 100644 doc/api/schema/AuthorizedKey.textile
 create mode 100644 doc/api/schema/Collection.html.textile.liquid
 delete mode 100644 doc/api/schema/Collection.textile
 create mode 100644 doc/api/schema/Commit.html.textile.liquid
 delete mode 100644 doc/api/schema/Commit.textile
 create mode 100644 doc/api/schema/CommitAncestor.html.textile.liquid
 delete mode 100644 doc/api/schema/CommitAncestor.textile
 create mode 100644 doc/api/schema/Group.html.textile.liquid
 delete mode 100644 doc/api/schema/Group.textile
 create mode 100644 doc/api/schema/Human.html.textile.liquid
 delete mode 100644 doc/api/schema/Human.textile
 create mode 100644 doc/api/schema/Job.html.textile.liquid
 delete mode 100644 doc/api/schema/Job.textile
 create mode 100644 doc/api/schema/JobTask.html.textile.liquid
 delete mode 100644 doc/api/schema/JobTask.textile
 create mode 100644 doc/api/schema/KeepDisk.html.textile.liquid
 delete mode 100644 doc/api/schema/KeepDisk.textile
 create mode 100644 doc/api/schema/Link.html.textile.liquid
 delete mode 100644 doc/api/schema/Link.textile
 create mode 100644 doc/api/schema/Log.html.textile.liquid
 delete mode 100644 doc/api/schema/Log.textile
 create mode 100644 doc/api/schema/Node.html.textile.liquid
 delete mode 100644 doc/api/schema/Node.textile
 create mode 100644 doc/api/schema/PipelineInstance.html.textile.liquid
 delete mode 100644 doc/api/schema/PipelineInstance.textile
 create mode 100644 doc/api/schema/PipelineTemplate.html.textile.liquid
 delete mode 100644 doc/api/schema/PipelineTemplate.textile
 create mode 100644 doc/api/schema/Repository.html.textile.liquid
 delete mode 100644 doc/api/schema/Repository.textile
 create mode 100644 doc/api/schema/Specimen.html.textile.liquid
 delete mode 100644 doc/api/schema/Specimen.textile
 create mode 100644 doc/api/schema/Trait.html.textile.liquid
 delete mode 100644 doc/api/schema/Trait.textile
 create mode 100644 doc/api/schema/User.html.textile.liquid
 delete mode 100644 doc/api/schema/User.textile
 create mode 100644 doc/api/schema/VirtualMachine.html.textile.liquid
 delete mode 100644 doc/api/schema/VirtualMachine.textile
 delete mode 100644 doc/index.html
 create mode 100644 doc/index.html.liquid
 create mode 100644 doc/install/client.html.textile.liquid
 delete mode 100644 doc/install/client.textile
 create mode 100644 doc/install/create-standard-objects.html.textile.liquid
 delete mode 100644 doc/install/create-standard-objects.textile
 create mode 100644 doc/install/index.html.md.liquid
 delete mode 100644 doc/install/index.md
 create mode 100644 doc/install/install-api-server.html.md
 delete mode 100644 doc/install/install-api-server.md
 create mode 100644 doc/install/install-crunch-dispatch.html.textile.liquid
 delete mode 100644 doc/install/install-crunch-dispatch.textile
 create mode 100644 doc/install/install-workbench-app.html.md
 delete mode 100644 doc/install/install-workbench-app.md
 create mode 100644 doc/sdk/index.html.textile.liquid
 delete mode 100644 doc/sdk/index.textile
 create mode 100644 doc/sdk/python/crunch-utility-libraries.html.textile.liquid
 delete mode 100644 doc/sdk/python/crunch-utility-libraries.textile
 create mode 100644 doc/sdk/python/python.html.textile.liquid
 delete mode 100644 doc/sdk/python/python.textile
 create mode 100644 doc/sdk/python/sdk-python.html.textile.liquid
 delete mode 100644 doc/sdk/python/sdk-python.textile
 create mode 100644 doc/user/examples/crunch-examples.html.textile.liquid
 delete mode 100644 doc/user/examples/crunch-examples.textile
 create mode 100644 doc/user/getting_started/check-environment.html.textile.liquid
 delete mode 100644 doc/user/getting_started/check-environment.textile
 create mode 100644 doc/user/getting_started/community.html.textile.liquid
 delete mode 100644 doc/user/getting_started/community.textile
 create mode 100644 doc/user/getting_started/ssh-access.html.textile.liquid
 delete mode 100644 doc/user/getting_started/ssh-access.textile
 create mode 100644 doc/user/getting_started/workbench.html.textile.liquid
 delete mode 100644 doc/user/getting_started/workbench.textile
 create mode 100644 doc/user/index.html.textile.liquid
 delete mode 100644 doc/user/index.textile
 create mode 100644 doc/user/reference/api-tokens.html.textile.liquid
 delete mode 100644 doc/user/reference/api-tokens.textile
 create mode 100644 doc/user/reference/sdk-cli.html.textile.liquid
 delete mode 100644 doc/user/reference/sdk-cli.textile
 create mode 100644 doc/user/tutorials/running-external-program.html.textile.liquid
 delete mode 100644 doc/user/tutorials/running-external-program.textile
 create mode 100644 doc/user/tutorials/tutorial-firstscript.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-firstscript.textile
 create mode 100644 doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-gatk-variantfiltration.textile
 create mode 100644 doc/user/tutorials/tutorial-job-debug.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-job-debug.textile
 create mode 100644 doc/user/tutorials/tutorial-job1.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-job1.textile
 create mode 100644 doc/user/tutorials/tutorial-keep.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-keep.textile
 create mode 100644 doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-new-pipeline.textile
 create mode 100644 doc/user/tutorials/tutorial-parallel.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-parallel.textile
 create mode 100644 doc/user/tutorials/tutorial-trait-search.html.textile.liquid
 delete mode 100644 doc/user/tutorials/tutorial-trait-search.textile
 create mode 100644 doc/zenweb-liquid.rb
 create mode 100644 doc/zenweb-textile.rb

       via  b54d7820e899733ce10b8960b1f04d0481f2e11f (commit)
       via  153d327346a213d0d48430af835b871ef4283da5 (commit)
       via  956093639196f92f3ad4b9e0795bcc7e30520e0d (commit)
       via  b54a5ea817d3d2087eaa07dcf98ec8a82af56d06 (commit)
       via  da51b9328abab2df757ed13eadc7c3557315094b (commit)
       via  7b66e00ebd071f5722ee18dcf132110020bdcdf3 (commit)
       via  3cd8626eda1618b9f2be293fc01c29f3d00973a7 (commit)
       via  3dc2b0008be4e09b47f73aeeb97d005cd7836619 (commit)
       via  91e4be41d77d023a06d53879b974ecf5d3b82d94 (commit)
       via  68ad3cbe4aaaa986b5b6e9f5cfcbf9d9d4c1c319 (commit)
      from  d0008ed3ab3c2cccb3b2aca217d4c86a1ad10cdd (commit)

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 b54d7820e899733ce10b8960b1f04d0481f2e11f
Merge: 153d327 d0008ed
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Feb 11 09:23:55 2014 -0500

    Merge branch 'master' of git.clinicalfuture.com:arvados


-----------------------------------------------------------------------


hooks/post-receive
-- 




More information about the arvados-commits mailing list