Hello Iry,

It seems that you need to update Cufflinks and include the helper script gtf_to_sam that comes with it. The current version supported by the wrappers available in galaxy-central and the latest galaxy-dist use version 1.3.0.


Details, including links to download locations, can be found at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

Please give this a try and let us know if you continue to have problems,

Best,

Jen
Galaxy team


On 10/19/12 12:22 PM, Iry Witham wrote:
Hi Folks,

I have run into an issue with cuffmerge.  I am attempting to run it with
mm10 references and it fails attempting to execute gtf_to_sam.  The
following is the actual error message I get:

Error running cuffmerge.
[Fri Oct 19 15:13:55 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Oct 19 15:13:55 2012] Preparing output location cm_output/
[Fri Oct 19 15:14:15 2012] Converting GTF files to SAM
gtf_to_sam: invalid option -- F
cufflinks v0.9.1
-----------------------------
Usage:   cufflinks [options] <transcripts.gtf> <out.sam
Options:

-r/--reference-seq                        reference fasta file for sequence 
bias correction     [ default:   NULL ]
        [FAILED]
Error: could not execute gtf_to_sam


I have assured that the indexes and loc files are correct and in place.  Can 
someone point me in the right direction?

Thanks,

Iry Witham

Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar
Harbor, ME  04609 Phone: 207-288-6744 email: iry.wit...@jax.org


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