Fusion Inspector Fusion Inspector Web Galaxyintegration Trinity fusion

Fusion. Inspector & Fusion. Inspector. Web 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 Defining a composite data type for Fusion. Inspector. Data, so that all the various output files of significance can be captured and used later for data navigation. Galaxy config/datatypes_conf. xml <!-- composite dataset with fusioninspector outputs in the extra files path --> <datatype extension="fusioninspectordata” type="galaxy. datatypes. fusioninspectordata: Fusion. Inspector. Data"> <display file="ctat/fusion_viewer. xml" /> </datatype> Module: lib/galaxy/datatypes/fusioninspectordata. py Implements 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 Fusion. Inspector Tool Galaxy tools/CTAT/fusion_inspector. xml <command interpreter='perl' > ### my $usage = "usage: $0 left. fq right. fq output_directorynn"; Fusion. Inspector_wrapper. pl Fusion. Inspector … params … ${fusion_inspector_data} >> "$out_log" </command> Fusion. Inspector_wrapper. pl (provided) runs Fusion. Inspector, 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 Fusion. Inspector. Web 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 Implementation Details: integration of Fusion. Inspector. Web 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> To construct the url that links out to Fusion. Inspector. Web, galaxy reads the ‘symtok. txt’ file stored in the composite data set and assigns that value as the URL parameter. Fusion. Inspector. Web then uses that parameter value to follow the corresponding symlink to the data to be served.