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> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
