Building and Running DGR

Building DGR

Check out the GeneRecommenderJava? project from CVS:
  • cvs checkout GeneRecommenderJava?

In the root of the checked-out directory GeneRecommenderJava? , build the project:
  • ant dist

If ant is not available in your PATH, ant is available in this directory:
  • /projects/sysbio/apps/x86_64/bin/Ant/apache-ant-1.7.0/bin

Running an Example Query

Here is an example command line to execute DGR with a single query:

  • java -Xmx500m -cp ./dist/dgr.jar edu.ucsc.bme.generecommender.dgr.DGRStandAlone Kegg_Proteasome.01.txt /projects/sysbio/cchen/DGR/Proteasome sce ygd 20 100 /projects/sysbio/cchen/Expression_Chad nonbatch yeast include_query 0 Kegg_Proteasome.txt Ranks/RankBased/Proteasome/rank

The output files are:
  • /projects/sysbio/cchen/DGR/Proteasome/Kegg_Proteasome.00.txt_sce.html
  • /projects/sysbio/cchen/DGR/Proteasome/Ranks/RankBased/Proteasome/rank_Kegg_Proteasome.01.txt

Explanation of the command line parameters:
  • To be supplied...

Command Line Parameters

This is the usage information generated by DGR:

  • Usage: java -Xmx500m java edu.ucsc.bme.generecommender.dgr.DGRStandAlone queryFileName queryFileLocation queryOrgName keyType nTopGene nTopExp expDataLocation batch|nonbatch speciesToUse [include_query|exclude_query] [pseudo_count] [expected_list_file] [expect_list_rank_file] [contrast_list_file]

Invoke the DGR executable
  • java -Xmx500m -cp ./dist/dgr.jar edu.ucsc.bme.generecommender.dgr.DGRStandAlone

With the following parameters:
  1. queryFileName
  2. queryFileLocation – Root directory for queryFileName, expect_list_rank_file, and contrast_list_file.
  3. queryOrgName
  4. keyType
  5. nTopGene
  6. nTopExp
  7. expDataLocation
  8. batch|nonbatch – Batch mode if parameter is "batch" (case-insensitive); otherwise, non-batch mode.
  9. speciesToUse
  10. [include_query|exclude_query] – Query genes are included in rank files if parameter begins with "include"; otherwise, query genes are excluded from the rank files.
  11. [pseudo_count] – Default value = 0.
  12. [expected_list_file] – One gene per line. Comment and blank lines ignored.
  13. [expect_list_rank_file] – Root name for output rank files.
  14. [contrast_list_file] – One gene per line. Comment and blank lines ignored.

Comment lines are indicated with "#" as the first non-whitespace character of a line.

-- DavidNg? - 19 Mar 2008