Dear all
We have constructed a workflow for analysing microarray data using
Soaplab web services (workflow attached). The idea is that the user
supplies a number of affymetrix CEL files (about 30Mb) via Taverna
which are then sent to the web services for analysis. Our problem
though is that we rapidly run out of memory (Java Heap space) when two
or more files are supplied. We have assigned more memory to Java, and
this helps, but clearly we are a long way from our goal of being able to
analyse tens of files. The solution would be use to references instead
of loading the files into memory but we cant find anything in the manual
that shows us how to do this. Any clues?
many thanks
Silvia Giuliani
<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0">
<s:workflowdescription lsid="urn:lsid:www.mygrid.org.uk:operation:3HN745VV5Z0" author="" title="" />
<s:processor name="affyclean">
<s:beanshell>
<s:scriptvalue>char space=' ';
int code=20; // this is the char code
// of the irritating ctrl char
char rubbish=(char) code;
String clean = CEL.replace(rubbish,space);</s:scriptvalue>
<s:beanshellinputlist>
<s:beanshellinput s:syntactictype="'text/plain'">CEL</s:beanshellinput>
</s:beanshellinputlist>
<s:beanshelloutputlist>
<s:beanshelloutput s:syntactictype="'text/plain'">clean</s:beanshelloutput>
</s:beanshelloutputlist>
</s:beanshell>
</s:processor>
<s:processor name="background" boring="true">
<s:stringconstant>mas</s:stringconstant>
</s:processor>
<s:processor name="normalize" boring="true">
<s:stringconstant>constant</s:stringconstant>
</s:processor>
<s:processor name="affyallocate">
<s:description>Allocates a space for affy-expresso analysis</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12852/axis/services/microarrays.affyallocate</s:soaplabwsdl>
</s:processor>
<s:processor name="filesuck">
<s:description>CEL file transfer</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12852/axis/services/microarrays.filesuck</s:soaplabwsdl>
</s:processor>
<s:processor name="affyexpresso">
<s:description>Bioconductor example using affy expresso (multiple CEL files via ref)</s:description>
<s:soaplabwsdl>http://devel.fec.cineca.it:12852/axis/services/microarrays.affyexpresso</s:soaplabwsdl>
</s:processor>
<s:processor name="Remove_duplicate_strings" boring="true">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates</s:local>
</s:processor>
<s:processor name="Merge_string_list_to_string" boring="true">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringListMerge</s:local>
</s:processor>
<s:link source="in1" sink="affyclean:CEL" />
<s:link source="Merge_string_list_to_string:concatenated" sink="affyexpresso:dir" />
<s:link source="Remove_duplicate_strings:strippedlist" sink="Merge_string_list_to_string:stringlist" />
<s:link source="Merge_string_list_to_string:concatenated" sink="out3" />
<s:link source="affyallocate:dir" sink="filesuck:indir" />
<s:link source="affyclean:clean" sink="filesuck:file1_direct_data" />
<s:link source="background:value" sink="affyexpresso:bgcorrect" />
<s:link source="filesuck:outdir" sink="Remove_duplicate_strings:stringlist" />
<s:link source="affyexpresso:result" sink="out" />
<s:link source="normalize:value" sink="affyexpresso:normalize" />
<s:source name="in1" />
<s:sink name="out" />
<s:sink name="out3" />
</s:scufl>
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