[Iplant-api-dev] No Output Agave Tutorial

[Pete Lawson]

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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