liyanhui607 wrote:

Dear Sir,

We have a program writen in perl. It can run nomally in linux environment with a file saved as result.

After added it to galaxy system, we found that it can produce the right result file in directary "/var/we/galaxy-dist/database/files/000" , but the result file did not return to the web page where the state is always "Job is currently running".

Could anyone tell me what is wrong ? why it does not work?

The bagging-SVM.xml and the bagging-SVM.pl are attached.

Thank you very much!

Best Wishes!

Yan-Hui Li

Hi Yan-Hui, If you leave the dataset running, does it eventually finish? If the output is extremely large it could be setting metadata on the output. You may want to try setting 'set_metadata_externally = True' in the config (universe_wsgi.ini). --nate

<tool id="bagging-SVM_1" name="bagging-SVM">

<description> Integration and co-expression network from the two features have the same reference gene prediction and functional genes </description> <command interpreter="perl">bagging-SVM.pl $infile_ref $infile_avedist1k $infile_corrgsea1k $outfile_all_positive </command> <inputs> <param format="text" name="infile_ref" type="data" label=" ../GO_angiogenesis_expressed20101024smr0.5_fppi.txt "/> <param format="text" name="infile_avedist1k" type="data" label=" ../expressed_genes_20101024.hprd8_biogrid-2.0.58.angiogenesis_avedist1k.txt "/> <param format="text" name="infile_corrgsea1k" type="data" label=" ../expressed_genes_20101024.hprd8_biogrid-2.0.58.angiogenesis_corrgsea1k.txt "/>

</inputs> <outputs> <data format="tabular" name="outfile_all_positive" label="outfile_all_positive"/> </outputs>

<tests> <test> <param name="input" value="1"/> <param name="input" value="../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt"/> <param name="input" value="../ppi/hprd8_biogrid-2.0.58.ppi.txt"/> <output name="out_file1" file="expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt"/> </test> </tests>

<help> Integration and co-expression network from the two features have the same reference gene prediction and functional genes </help>

</tool>

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