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
bagging-SVM.pl
Description: Binary data
<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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