PomBase / Chado / #305 run GO jenkins checks on Canto

#305 run GO jenkins checks on Canto

Milestone: next-load

Status: open

Owner: Kim Rutherford

Labels: logs (30)

Priority: 3

Updated: 2014-04-06

Created: 2014-03-20

Creator: Valerie Wood

Private: No

No great urgency, but some time

Discussion

Midori Harris - 2014-03-26

I've got this running on my desktop now; it turned out to be dead easy, so holler if you want any pointers.

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- Kim Rutherford - 2014-04-01
  
  Great. That will be very helpful. If you have any notes or command line examples, could you add them to this ticket?
  
  Cheers.
  
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Midori Harris - 2014-03-28

labels: --> logs

summary: QC run GO jenkins checks on Canto --> run GO jenkins checks on Canto

Description has changed:

Diff:

--- old +++ new @@ -1,3 +1,2 @@ - No great urgency, but some time

assigned_to: Kim Rutherford
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Midori Harris - 2014-04-02

Sorry didn't get round to this yesterday ...

Download & install owltools for the command line. I followed the "Building from Source" instructions here and it seemed to work fine:

http://code.google.com/p/owltools/wiki/InstallOWLTools

Once you've done that, you can either add to $PATH as suggested or issue the command as /path/to/owltools.

This beasty does the same GAF checks as the GO Jenkins setup. Remove the newlines so it's all one big command. You'll also have to replace "/path/to/go/" and "/path/to/output/" with the actual paths (obviously):

% owltools --catalog-xml /path/to/go/go_svn/ontology/extensions/catalog-v001.xml http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl --gaf /path/to/go/go_svn/gene-associations/submission/gene_association.pombase.gz --gaf-report-file /path/to/output/gaf-validation-report.txt --gaf-report-summary-file /path/to/output/gaf-validation-summary.txt --gaf-prediction-file /path/to/output/gene_association.pombase.inf.gaf --gaf-prediction-report-file /path/to/output/gaf-prediction-report.txt --experimental-gaf-prediction-file /path/to/output/gene_association.pombase.experimental.gaf --experimental-gaf-prediction-report-file /path/to/output/gaf-prediction-experimental- report.txt --gaf-run-checks
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Kim Rutherford - 2014-04-06

run GO jenkins checks on Canto

Would it be OK to run these checks when loading Chado and add a new log file? It would be a convenient to run it as part of the usual load.

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Midori Harris - 2014-04-06

yep, that would make perfect sense

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