Story #10499

[Doc] Improve user guide for CWL with Crunch2

Added by Tom Morris almost 5 years ago. Updated almost 5 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
11/09/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
1.0

Description

- mark non-CWL related things as deprecated/legacy
- document any user visible differences between crunch1 and crunch2
- review for consistency with current feature set


Subtasks

Task #10505: ReviewResolvedTom Clegg


Related issues

Related to Arvados - Story #10604: Additional Crunch2 CWL User Guide updatesResolved11/23/2016

Associated revisions

Revision 78889e11
Added by Tom Clegg almost 5 years ago

Merge branch '10499-cwl-crunch2-docs' refs #10499

History

#1 Updated by Tom Clegg almost 5 years ago

  • Project changed from Arvados Private to Arvados

#2 Updated by Tom Clegg almost 5 years ago

Workbench > "Running a pipeline using Workbench"
  • "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On those sites, the details will be slightly different and the example pipelines might not be available."
CLI > "Running an Arvados pipeline"
  • "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On newer installations, use Common Workflow Language instead.
CLI > "Using arv-run"
  • "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On those sites, the features described here are not yet implemented."

#3 Updated by Tom Clegg almost 5 years ago

  • Status changed from New to In Progress

#4 Updated by Tom Clegg almost 5 years ago

  • Assigned To changed from Tom Clegg to Radhika Chippada

work in progress on 10499-cwl-crunch2-docs

#5 Updated by Radhika Chippada almost 5 years ago

A few ideas (I can work on these, once we agree on the list of changes to be made):

Run a pipeline using Workbench section:

  • Rename as "Using Crunch" or something like that
  • Move "Introduction to Crunch" from "Develop an Arvados Pipeline" as the first item in this section
  • Add a new page "Running a workflow using Workbench" after "Accessing workbench". This would of course need adding a tutorial workflow to qr1hi and authoring this page etc
  • Rename "Running a pipeline using workbench" as "Running a pipeline using workbench (Deprecated)"

user/tutorials/tutorial-keep.html

  • diagram under "Locate your collection in Workbench" has wrong tab title for pipelines tab (and the other diagram too, but it is not too apparent here)

topics/arv-copy.html

  • How to copy a pipeline template => Do we need to add any notes here about workflows? Otherwise, add a "How to copy a workflow" section?

user/cwl/cwl-runner.html

  • Registering a workflow with Workbench => "Use --create-template to register a CWL workflow" -- use "--create-workflow" instead?

Working on the command line

  • Append "(Deprecated)" to both page titles?
  • Do we want to add a page to work with container_requests and / or workflows here?

Develop an Arvados pipeline

  • Rename it as "Develop an Arvados pipeline (Deprecated)" ?
  • This would need moving a couple pages.
    • Move "Introduction to Crunch" to the top of the list as noted in the first comment
    • Add a new "Docker" section and move "Customizing Crunch environment using Docker" into it?

#6 Updated by Radhika Chippada almost 5 years ago

Tom: please go ahead and merge 10499-cwl-crunch2-docs branch into master. I do not see any objectionable issues with your updates. Thanks.

#7 Updated by Tom Morris almost 5 years ago

  • Status changed from In Progress to Resolved
  • Assigned To changed from Radhika Chippada to Tom Clegg

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