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BD2KGenomics / dcc-action-service

A place for our business logic written in Luigi that triggers workflow launches.
Apache License 2.0
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Rna seqdecider #1

Closed wshands closed 7 years ago

wshands commented 7 years ago

Brian, please take a look at this RNASeq script. I tested it by making a call to Luigi. PYTHONPATH='..' luigi --module RNASeqTask RNASeqCoordinator --redwood-client-path ../../../redwood-client/ucsc-storage-client/ --redwood-host storage.ucsc-cgl.org --redwood-token --local-scheduler --tmp-dir pwd/luigi_state --data-dir $(pwd) --max-jobs 400 1> stdout.txt 2> stderr.txt

The problem I see is that the script seems to run twice. I still have to debug this. There are a couple of other points:

  1. I had to instruct urlopen to ignore certs due to the non self signed certs issue
  2. I do not know where we will have rsem, kallisto and star so I default them to the cwd
  3. The data file location setup in the json around line 71 will need to be changed