Chris, The problem is likely a bug in the Cufflinks wrapper that was recently fixed in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60 Try updating your Galaxy instance to include this changeset; if this doesn't fix the problem, let us know. Good luck, J. On Nov 11, 2011, at 10:44 AM, Bidwell, Christopher A. wrote: > Colleagues, > > 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 > /phillip/hiscansq/run00085-09-16-11_D0D1KACXX/110916_H179_0062_AD0D1KACXX/hr00206_OAR13-24/References/Bos_taurus/genome.fa > > 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. > Chris > ___________________________________________________________ > 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/
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