[Iplant-api-dev] No Output Agave Tutorial

[Barthelson, Roger A - (rogerab)]

I think an output file should be defined, and you use the -o setting of samtools sort to set the name. A fix named should be used so that the output can be used in a workflow. But I don’t think the lack of the output file setting was the reason samtools failed. It clearly did not see some required input to run, or otherwise the command line had something it couldn’t interpret. So if your wrapper is okay, then there is something likely wrong with the json for defining the app.

Roger
--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>


On August 1, 2014 at 8:35:16 AM, Pete Lawson (geekypete at gmail.com<mailto:geekypete at gmail.com>) wrote:

Hello all!

I am working my way through the Agave tutorial on GitHub https://github.com/iPlantCollaborativeOpenSource/iplant-agave-sdk and have managed to get all the way up to running the Sam-Tools-Sort staged from my iPlant datastore. The problem I was running into is that it is not generating the sorted.bam file that I expect. All the other expected files are generated. The .err log displays the following message:

{
  "status" : "success",
  "message" : null,
  "version" : "2.0.0-SNAPSHOT-r6cf80",
  "result" : { }
}
Usage:   samtools sort [options] <in.bam> <out.prefix>

Options: -n        sort by read name
         -f        use <out.prefix> as full file name instead of prefix
         -o        final output to stdout
         -l INT    compression level, from 0 to 9 [-1]
         -@ INT    number of sorting and compression threads [1]
         -m INT    max memory per thread; suffix K/M/G recognized [768M]

{
  "status" : "success",
  "message" : null,
  "version" : "2.0.0-SNAPSHOT-r6cf80",
  "result" : { }
}

This gives me the impression that the JSON is not properly defined and the correct command line parameters are not being passed to samtools. I see that the samtools-sort-job.json provided in the example does not define an output filename or path. Do I need to amend the job submission JSON to accommodate this?

Thanks!
-Pete Lawson

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