Mercurial > repos > fubar > rg_gsea

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## Galaxy GSEA wrapper failure<br/>
## Unable to find index.html in [] - listdir=gsea_test.rnk gsea_test.gmt gseatestout jun10 gsea_runner.log<br/>
## Command line was java -Xmx6G -cp /home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar xtools.gsea.GseaPreranked -gmx /home/rlazarus/galaxy-central/tools/rgGSEA/test-data/gseatestout/gsea_test.gmt -gui false -make_sets true -rnd_seed timestamp -norm meandiv -zip_report false -scoring_scheme weighted -rnk /home/rlazarus/galaxy-central/tools/rgGSEA/test-data/gseatestout/gsea_test.rnk -out gseatestout -set_max 500 -set_min 15 -mode Max_probe -collapse false -nperm 10 -rpt_label GSEAtest -plot_top_x 20<br/>
## commonly caused by mismatched ID/chip selection<br/>
## gsea_runner.log=java.io.FileNotFoundException: File not found: /home/rlazarus/galaxy

	at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(EIKM)

	at edu.mit.broad.genome.parsers.ParserFactory.read(EIKM)

	at xtools.api.param.PobParam.getPob(EIKM)

	at xtools.api.param.RankedListReqdParam.getRankedList(EIKM)

	at xtools.gsea.GseaPreranked.createHeader(EIKM)

	at xtools.gsea.GseaPreranked.execute(EIKM)

	at xtools.api.AbstractTool.tool_main(EIKM)

	at xtools.gsea.GseaPreranked.main(EIKM)

java.io.FileNotFoundException: File not found: /home/rlazarus/galaxy

	at edu.mit.broad.genome.parsers.ParserFactory.createInputStream(EIKM)

	at edu.mit.broad.genome.parsers.ParserFactory.read(EIKM)

	at xtools.api.param.PobParam.getPob(EIKM)

	at xtools.api.param.RankedListReqdParam.getRankedList(EIKM)

	at xtools.gsea.GseaPreranked.execute(EIKM)

	at xtools.api.AbstractTool.tool_main(EIKM)

	at xtools.gsea.GseaPreranked.main(EIKM)

7770 [INFO ] Renaming rpt dir on error to: gseatestout/error_GSEAtest.GseaPreranked.1370827107649
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author	fubar
date	Sun, 09 Jun 2013 23:09:34 -0400
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