[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
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create mode 100644 doc/install/install-workbench-app.html.md
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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
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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
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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
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