FusionInspector & FusionInspectorWeb Galaxy-integration

Trinity fusion transcripts (fasta)

Fusion Inspector summary (tab-delim)

Log file for run

Fusion Inspector Results (package)

Trinity fusion transcripts (fasta)

Fusion Inspector summary (tab-delim)

Click the link to visit the Fusion Inspector Web portal.

Fusion Inspector Web (powered by IGV.js)

Galaxy Implementation details: defining the data type

Galaxy config/datatypes_conf.xml

<!-- composite dataset with fusioninspector outputs in the extra files path --> <datatype extension="fusioninspectordata” type="galaxy.datatypes.fusioninspectordata:FusionInspectorData"> <display file="ctat/fusion_viewer.xml" /> </datatype>

Defining a composite data type for FusionInspectorData, so that all the various output files of significance can be captured and used later for data navigation.

Module: lib/galaxy/datatypes/fusioninspectordata.pyImplements the data type definition. (note, the only thing this module does that is of any importance is to set the data type as composite)

Galaxy Implementation Details: Specifying the FusionInspector Tool

Galaxy tools/CTAT/fusion_inspector.xml

<command interpreter='perl' >### my $usage = "usage: $0 left.fq right.fq output_directory\n\n";FusionInspector_wrapper.plFusionInspector … params …${fusion_inspector_data}>> "$out_log" </command>

FusionInspector_wrapper.pl (provided) runs FusionInspector, copies the output files to the galaxy/database/files/… directory according to expectations for a composite data type, and it creates a symlink to this data output directory that is stored in an apache webserver directory for later access by the FusionInspectorWeb portal.

For ‘security purposes’, the name of the symlink is randomly generated and stored in the output directory as ‘symtok.txt’ (further needed for galaxy integration – see next slide on visualization adaptor)

Galaxy display_applications/ctat/fusion_viewer.xml

<display id='FIweb' version='0.0.1' name='Fusion Inspector Web' > <link id='main' name='main'> <url>http://caique.broadinstitute.org/FIWeb_galaxy.cgi?dataset=${symtok.qp}</url> <param type='data' name='my_param' />

<param type="template" name="symtok" strip="True" > #set myfilename = $my_param.value.extra_files_path + "/symtok.txt" #set code = open(myfilename).readline().rstrip() ${code} </param>

</link></display>

Galaxy Implementation Details: integration of FusionInspectorWeb

To construct the url that links out to FusionInspectorWeb, galaxy reads the ‘symtok.txt’ file stored in the composite data set and assigns that value as the URL parameter.

FusionInspectorWeb then uses that parameter value to follow the corresponding symlink to the data to be served.