We have set up a local Galaxy but I am having trouble running Cufflinks with 
the annotation gtf file.  We have the iGenomes btau4.2 genome in the database 
and use the iGenomes btau4.2 gtf file in the history.  However the –G isn’t 
showing up in the command line (below) and the output is the same as when I run 
cufflinks without annotation.
Is something not set up correctly?
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 4 -N -b 
The details page shows the gtf file being supplied from the history

Input Parameter              Value
SAM or BAM file of aligned RNA-Seq reads          26: Tophat for Illumina on 
data 2 and data 1: accepted_hits
Max Intron Length          50000
Min Isoform Fraction      0.05
Pre MRNA Fraction         0.05
Perform quartile normalization Yes
Conditional (reference_annotation)       1
Reference Aonnotation                24: Btau42_iGenomes_annot.gtf
Conditional (bias_correction)     0
Conditional (seq_source)             0
Conditional (singlePaired)            0

Thanks for your help.
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