Hi, Sarah. The message you saw:

AssertionError: ##rgFastQC.py error - cannot find executable /Users/allabyrg/Desktop/galaxy-dist/tool-data/shared/jars/FastQC/fastqc

suggests that the wrapper can't find the required FastQC perl wrapper called fastqc. For complicated reasons, it needs to be available as part of a complete FastQC installation as it calls the various java components and expects to find them where the FastQC distribution puts them. Please try unpacking the FastQC distribution archive into that .../tool-data/shared/jars directory - no galaxy restart required - and see if that helps? On Wed, Nov 9, 2011 at 9:35 AM, Palmer, Sarah <S.A.Palmer@warwick.ac.uk> wrote:

Hi, I have been trying to run fastqc on our standalone installations of Galaxy and repeatedly get the attached error message. I have tried this now with both 454 and Illumina fastq files, on 2 different Mac Machines with 10.5 and 10.6 OS and Python versions 2.5 and 2.7 on one of the machines and get the same problem occurring each time. Could you please help me find a fix for this? Cheers, Sarah ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;