[ARVADOS] updated: eb3c52158a603946b7680ae5f3f0848c7246eb9c
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 30 12:04:47 EDT 2014
Summary of changes:
doc/_config.yml | 1 +
doc/_includes/_alert_docker.liquid | 4 -
.../schema/PipelineTemplate.html.textile.liquid | 6 +-
doc/install/index.html.textile.liquid | 2 -
doc/install/install-docker.html.textile.liquid | 94 ++++++------
.../check-environment.html.textile.liquid | 2 +-
docker/api/Dockerfile | 37 ++++-
docker/api/application.yml.in | 5 +
docker/api/apt.arvados.org.list | 2 +
docker/api/arvados-clients.yml.in | 5 +
docker/api/crunch-dispatch-run.sh | 24 +++
docker/api/keep_server_0.json | 6 +
docker/api/keep_server_1.json | 7 +
docker/api/munge.key | Bin 0 -> 1024 bytes
docker/api/setup-gitolite.sh.in | 77 ++++++++++
docker/api/setup.sh.in | 62 ++++++++
docker/api/slurm.conf.in | 60 ++++++++
docker/api/supervisor.conf | 29 ++++
docker/api/update-gitolite.rb | 162 +++++++++++++++++++++
docker/arvdock | 120 ++++++++++++---
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 32 +++-
docker/build_tools/Makefile | 143 ++++++++++++++++--
docker/build_tools/build.rb | 28 +++-
docker/compute/Dockerfile | 28 ++++
docker/compute/fuse.conf | 10 ++
docker/compute/setup.sh.in | 20 +++
docker/{api => compute}/ssh.sh | 0
docker/compute/supervisor.conf | 29 ++++
docker/compute/wrapdocker | 90 ++++++++++++
docker/config.yml.example | 4 +
docker/shell/Dockerfile | 19 +++
docker/shell/fuse.conf | 10 ++
docker/shell/setup.sh.in | 21 +++
docker/{api => shell}/superuser_token.in | 0
docker/shell/supervisor.conf | 15 ++
docker/slurm/Dockerfile | 11 ++
docker/slurm/munge.key | Bin 0 -> 1024 bytes
docker/slurm/slurm.conf.in | 60 ++++++++
docker/slurm/supervisor.conf | 14 ++
docker/workbench/Dockerfile | 3 +
sdk/python/arvados/commands/put.py | 21 +--
sdk/python/arvados/keep.py | 139 +++++++++++-------
sdk/python/bin/arv-ls | 2 +-
.../api/app/controllers/application_controller.rb | 1 +
46 files changed, 1247 insertions(+), 164 deletions(-)
delete mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 docker/api/apt.arvados.org.list
create mode 100644 docker/api/arvados-clients.yml.in
create mode 100755 docker/api/crunch-dispatch-run.sh
create mode 100644 docker/api/keep_server_0.json
create mode 100644 docker/api/keep_server_1.json
create mode 100644 docker/api/munge.key
create mode 100755 docker/api/setup-gitolite.sh.in
create mode 100755 docker/api/setup.sh.in
create mode 100644 docker/api/slurm.conf.in
create mode 100755 docker/api/update-gitolite.rb
create mode 100644 docker/base/apt.arvados.org.list
create mode 100644 docker/compute/Dockerfile
create mode 100644 docker/compute/fuse.conf
create mode 100755 docker/compute/setup.sh.in
copy docker/{api => compute}/ssh.sh (100%)
create mode 100644 docker/compute/supervisor.conf
create mode 100755 docker/compute/wrapdocker
create mode 100644 docker/shell/Dockerfile
create mode 100644 docker/shell/fuse.conf
create mode 100755 docker/shell/setup.sh.in
copy docker/{api => shell}/superuser_token.in (100%)
create mode 100644 docker/shell/supervisor.conf
create mode 100644 docker/slurm/Dockerfile
create mode 100644 docker/slurm/munge.key
create mode 100644 docker/slurm/slurm.conf.in
create mode 100644 docker/slurm/supervisor.conf
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commit eb3c52158a603946b7680ae5f3f0848c7246eb9c
Author: radhika <radhika at curoverse.com>
Date: Wed Jul 30 12:04:11 2014 -0400
3016: Update per Tom's review feedback.
diff --git a/doc/api/schema/PipelineTemplate.html.textile.liquid b/doc/api/schema/PipelineTemplate.html.textile.liquid
index b23d01c..a16ed51 100644
--- a/doc/api/schema/PipelineTemplate.html.textile.liquid
+++ b/doc/api/schema/PipelineTemplate.html.textile.liquid
@@ -21,14 +21,14 @@ table(table table-bordered table-condensed).
|default |any |any |The default value for this parameter.|
|required |boolean |true or false |Specifies whether the parameter is required to have a value or not.|
|dataclass |string |One of 'Collection', 'File' [1], 'number', or 'text' |Data type of this parameter.|
-|search_for |string |any string |Substring to look for in input collection or file name identifier.|
+|search_for |string |any string |Substring to use as a default search string when choosing inputs.|
|output_of |string |the name of another component in the pipeline |Specifies that the value of this parameter should be set to the 'output' attribute of the job that corresponds to the specified component.|
The 'output_of' parameter is especially important, as this is how components are actually linked together to form a pipeline. Component jobs that depend on the output of other components do not run until the parent job completes and has produced output. If the parent job fails, the entire pipeline fails.
fn1. The 'File' type refers to a specific file within a Keep collection in the form 'collection_hash/filename', for example '887cd41e9c613463eab2f0d885c6dd96+83/bob.txt'.
-The 'search_for' parameter is meaningful only when input dataclass of type Collection or File is used. If a value is provided, this will be preloaded into the input data chooser dialog. For example, if your input dataclass is a File and you are interested in a certain filename exetention, you can preconfigure it in this attribute.
+The 'search_for' parameter is meaningful only when input dataclass of type Collection or File is used. If a value is provided, this will be preloaded into the input data chooser dialog in Workbench. For example, if your input dataclass is a File and you are interested in a certain filename extention, you can preconfigure it in this attribute.
h3. Examples
@@ -46,7 +46,7 @@ This is a pipeline named "Filter MD5 hash values" with two components, "do_hash"
"input": {
"required": true,
"dataclass": "Collection",
- "search_for": "FASTQ"
+ "search_for": ".fastq.gz"
}
},
},
commit f63a84da333cbcf898fabd41667051f09fae1117
Merge: 9cff219 20f944b
Author: radhika <radhika at curoverse.com>
Date: Wed Jul 30 11:36:55 2014 -0400
Merge branch 'master' into 3016-pipeline-template-search-string
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