[ARVADOS] updated: 189fee6586b290a78cdc1b3a3b9845efe0cf7499
git at public.curoverse.com
git at public.curoverse.com
Wed Mar 12 14:42:19 EDT 2014
Summary of changes:
.../app/controllers/application_controller.rb | 16 ++--
.../notifications/_pipelines_notification.html.erb | 2 +-
doc/README | 28 +++++
doc/Rakefile | 9 ++
doc/_config.yml | 22 +++-
doc/_includes/_run_md5sum_py.liquid | 33 ++----
doc/_includes/_tutorial_hash_script_py.liquid | 72 ++++-------
doc/_includes/_webring.liquid | 29 +++++
doc/_layouts/default.html.liquid | 8 +-
doc/admin/cheat_sheet.html.textile.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 2 +-
doc/api/index.html.textile.liquid | 2 +-
doc/api/methods.html.textile.liquid | 2 +-
.../api_client_authorizations.html.textile.liquid | 2 +-
doc/api/methods/api_clients.html.textile.liquid | 2 +-
.../methods/authorized_keys.html.textile.liquid | 2 +-
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/groups.html.textile.liquid | 2 +-
doc/api/methods/humans.html.textile.liquid | 2 +-
doc/api/methods/job_tasks.html.textile.liquid | 2 +-
doc/api/methods/jobs.html.textile.liquid | 2 +-
doc/api/methods/keep_disks.html.textile.liquid | 2 +-
doc/api/methods/links.html.textile.liquid | 2 +-
doc/api/methods/logs.html.textile.liquid | 2 +-
doc/api/methods/nodes.html.textile.liquid | 2 +-
.../methods/pipeline_instances.html.textile.liquid | 2 +-
.../methods/pipeline_templates.html.textile.liquid | 2 +-
doc/api/methods/repositories.html.textile.liquid | 2 +-
doc/api/methods/specimens.html.textile.liquid | 2 +-
doc/api/methods/traits.html.textile.liquid | 2 +-
doc/api/methods/users.html.textile.liquid | 2 +-
.../methods/virtual_machines.html.textile.liquid | 2 +-
doc/api/permission-model.html.textile.liquid | 2 +-
doc/api/resources.html.textile.liquid | 2 +-
doc/api/schema/ApiClient.html.textile.liquid | 2 +-
.../ApiClientAuthorization.html.textile.liquid | 2 +-
doc/api/schema/AuthorizedKey.html.textile.liquid | 2 +-
doc/api/schema/Collection.html.textile.liquid | 2 +-
doc/api/schema/Commit.html.textile.liquid | 2 +-
doc/api/schema/CommitAncestor.html.textile.liquid | 2 +-
doc/api/schema/Group.html.textile.liquid | 2 +-
doc/api/schema/Human.html.textile.liquid | 2 +-
doc/api/schema/Job.html.textile.liquid | 2 +-
doc/api/schema/JobTask.html.textile.liquid | 2 +-
doc/api/schema/KeepDisk.html.textile.liquid | 2 +-
doc/api/schema/Link.html.textile.liquid | 2 +-
doc/api/schema/Log.html.textile.liquid | 2 +-
doc/api/schema/Node.html.textile.liquid | 2 +-
.../schema/PipelineInstance.html.textile.liquid | 2 +-
.../schema/PipelineTemplate.html.textile.liquid | 2 +-
doc/api/schema/Repository.html.textile.liquid | 2 +-
doc/api/schema/Specimen.html.textile.liquid | 2 +-
doc/api/schema/Trait.html.textile.liquid | 2 +-
doc/api/schema/User.html.textile.liquid | 2 +-
doc/api/schema/VirtualMachine.html.textile.liquid | 2 +-
doc/css/code.css | 27 ++++
doc/css/nav-list.css | 4 +
.../pipeline_templates/gatk-exome-fq-snp.json | 85 ++++++++-----
doc/index.html.liquid | 10 +-
doc/install/client.html.textile.liquid | 2 +-
.../create-standard-objects.html.textile.liquid | 2 +-
.../install-crunch-dispatch.html.textile.liquid | 2 +-
doc/sdk/index.html.textile.liquid | 5 +-
.../crunch-utility-libraries.html.textile.liquid | 2 -
doc/sdk/python/sdk-python.html.textile.liquid | 2 -
.../examples/crunch-examples.html.textile.liquid | 4 -
.../check-environment.html.textile.liquid | 6 -
.../getting_started/community.html.textile.liquid | 4 -
.../getting_started/ssh-access.html.textile.liquid | 9 +-
.../getting_started/workbench.html.textile.liquid | 7 +-
doc/user/index.html.textile.liquid | 18 ++--
doc/user/reference/api-tokens.html.textile.liquid | 6 +-
doc/user/reference/sdk-cli.html.textile.liquid | 3 -
doc/user/topics/keep.html.textile.liquid | 48 +++++++
...nning-pipeline-command-line.html.textile.liquid | 119 ++++++++++++++++++
...rial-gatk-variantfiltration.html.textile.liquid | 6 +-
.../tutorial-job-debug.html.textile.liquid | 15 +--
.../tutorial-job1.html.textile.liquid | 46 +++-----
.../tutorial-parallel.html.textile.liquid | 19 +--
.../tutorial-trait-search.html.textile.liquid | 4 -
.../tutorials/intro-crunch.html.textile.liquid | 17 +++
.../running-external-program.html.textile.liquid | 46 +++----
.../tutorial-firstscript.html.textile.liquid | 72 ++++++-----
.../tutorials/tutorial-keep.html.textile.liquid | 93 ++++++++++-----
.../tutorial-new-pipeline.html.textile.liquid | 129 ++++----------------
...tutorial-pipeline-workbench.html.textile.liquid | 25 ++++
doc/zenweb-liquid.rb | 33 +++++-
sdk/cli/bin/arv-run-pipeline-instance | 3 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 4 +-
.../api/config/initializers/omniauth.rb.example | 2 +-
91 files changed, 704 insertions(+), 488 deletions(-)
create mode 100644 doc/README
create mode 100644 doc/_includes/_webring.liquid
create mode 100644 doc/css/code.css
create mode 100644 doc/user/topics/keep.html.textile.liquid
create mode 100644 doc/user/topics/running-pipeline-command-line.html.textile.liquid
rename doc/user/{tutorials => topics}/tutorial-gatk-variantfiltration.html.textile.liquid (98%)
rename doc/user/{tutorials => topics}/tutorial-job-debug.html.textile.liquid (96%)
rename doc/user/{tutorials => topics}/tutorial-job1.html.textile.liquid (74%)
rename doc/user/{tutorials => topics}/tutorial-parallel.html.textile.liquid (71%)
rename doc/user/{tutorials => topics}/tutorial-trait-search.html.textile.liquid (99%)
create mode 100644 doc/user/tutorials/intro-crunch.html.textile.liquid
create mode 100644 doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
via 189fee6586b290a78cdc1b3a3b9845efe0cf7499 (commit)
via 850bcd4de3903186ace4fe00a67d6c0910c959c2 (commit)
via 394c762a07ac25c9db586a614ef44045291edd72 (commit)
via d2789e22edd47adb747721ea20c76a607c9650d1 (commit)
via db1aad98d37e1e5930618336b50111ec836ba5d7 (commit)
via 9bdde1c9f875bab4e0bfee5e2259cc40b315ce68 (commit)
via adea7dcb58e33e4667ae228845b6a4c1bfb920f0 (commit)
via e4f96fc61cd9c85f91bdb0020bc365f2f4825ffb (commit)
via 927d11b99091dc4493446681209bec514c92f1bf (commit)
via 8c90084189d5ddb42359688aabd57f77ae867000 (commit)
via 4d3ece2c9b2b840a2899c03be215bf222fd52b13 (commit)
via 0191262856619bfaaa62629cc2f0b0ef15b5b9a2 (commit)
via 024bc6551b9d06a5fa9a8aa7c71ce1895e8a0ede (commit)
via 9a3fd18942055b0ec78f85aad3df4bbd2cc4f548 (commit)
via aa961ea35ffb01f88777d8e86336627e88da725d (commit)
via e86868d96caea7af41140e9d3e26f40b144a0ff6 (commit)
via 9ab861b00881ea7a5737d89b90ad17ceb264c8da (commit)
via fdbef7b63085492ddbc9201726508d63d0c8bf8f (commit)
via 4638e5fd00707c755c685bf601f92d27038703f3 (commit)
via 15dd4bd9a033b3ca45774994a84fe1bfa2226655 (commit)
via 55d96c71c561e51e8a00974caf60123698fc0647 (commit)
via a0bcef395615dc00d3b14d6f33a802e789d571e4 (commit)
via c592425e9ce54bee52f825c1ec1d2caa665ba308 (commit)
via a7f378b2267ddc1b44a8661d6723264fe959d98e (commit)
via 3fb3557b13cce8fee3bab0f81ab03b78fbef67dd (commit)
via 005928e7cbe6abbe418588f3eb652b3dee16e544 (commit)
via 88b5b089f38a587292bb68772251b8275c0e27c7 (commit)
via 491f4f3023d0f45be94e5f7091da85094e887212 (commit)
via 7791c7e1b09341ce1fed131c6b11c91da8217c3f (commit)
via cc414357e4eda3ed2060307f5b821385ae3d74bb (commit)
from 041a71c199e15f89b5adf4a5b5058b5ccbb171ee (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 189fee6586b290a78cdc1b3a3b9845efe0cf7499
Merge: 041a71c 850bcd4
Author: Tim Pierce <twp at curoverse.com>
Date: Wed Mar 12 14:43:38 2014 -0400
Merge branch 'master' into 2221-complete-docker
Conflicts:
doc/user/topics/tutorial-job-debug.html.textile.liquid
doc/user/tutorials/tutorial-keep.html.textile.liquid
diff --cc doc/user/topics/tutorial-job-debug.html.textile.liquid
index 3a3cbac,0974e51..a28a793
--- a/doc/user/topics/tutorial-job-debug.html.textile.liquid
+++ b/doc/user/topics/tutorial-job-debug.html.textile.liquid
@@@ -109,8 -105,8 +105,8 @@@ EOF</span
2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578 check slurm allocation
2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578 node localhost - 1 slots
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 start
-2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script hello-world.py
+2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script hello-world-fixed.py
- 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_version /home/you/you
+ 2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_version /home/<b>you</b>/<b>you</b>
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_parameters {}
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 runtime_constraints {"max_tasks_per_node":0}
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 start level 0
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list