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Idea #2991

closed

[Sample pipelines] Make the multi-component bcbio-nextgen pipeline template work

Added by Tom Clegg almost 10 years ago. Updated about 7 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Peter Amstutz
Category:
-
Target version:
-
Start date:
06/27/2014
Due date:
Story points:
3.0

Description

https://github.com/chapmanb/bcbio-nextgen

Subtasks 6 (0 open — 6 closed)

Task #3110: Write scripts using bcbio-nextgen ResolvedPeter Amstutz06/27/2014Actions
Task #3109: Inject arvados sdk into bcbio docker imageResolvedPeter Amstutz06/27/2014Actions
Task #3175: Review 2991-job-docker-imagesResolvedPeter Amstutz06/27/2014Actions
Task #3111: Run on AWS ResolvedPeter Amstutz06/27/2014Actions
Task #3108: Build bcbio-nextgen docker imageResolvedPeter Amstutz06/27/2014Actions
Task #3230: Support bcbio parallelization frameworkClosedPeter Amstutz06/27/2014Actions
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 #1

Updated by Tom Clegg almost 10 years ago

  • Story points changed from 3.0 to 5.0
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 #2

Updated by Tom Clegg almost 10 years ago

  • Target version set to 2014-07-16 Sprint
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 #3

Updated by Peter Amstutz almost 10 years ago

  • Assigned To set to Peter Amstutz
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 #4

Updated by Peter Amstutz almost 10 years ago

  • Description updated (diff)
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 #5

Updated by Tim Pierce almost 10 years ago

Review at 0b8f1f94:

  • docker/bcbio-nextgen/Dockerfile
    • "FROM bcbio-nextgen" - When I attempt to build, docker dies with a 404 error when it can't find this image. arvados/jobs maybe?
  • docker/build_tools/Makefile
    • BCBIO_NEXTGEN_DEPS is not defined (if it's intentionally empty, that's okay but please define it explicitly somewhere)
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 #6

Updated by Tom Clegg almost 10 years ago

  • Status changed from New to In Progress
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 #7

Updated by Ward Vandewege almost 10 years ago

  • Target version changed from 2014-07-16 Sprint to 2014-08-06 Sprint
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 #8

Updated by Tom Clegg almost 10 years ago

  • Subject changed from Make bcbio-nextgen pipeline template to [Sample pipelines] Make the multi-component bcbio-nextgen pipeline template work
  • Story points changed from 5.0 to 3.0
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 #9

Updated by Tom Clegg almost 10 years ago

  • Target version changed from 2014-08-06 Sprint to Arvados Future Sprints
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 #10

Updated by Peter Amstutz almost 8 years ago

  • Status changed from In Progress to Resolved
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 #11

Updated by Tom Clegg about 7 years ago

  • Target version deleted (Arvados Future Sprints)
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