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Question: Application Error
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gravatar for Palmer, Sarah
7.1 years ago by
Palmer, Sarah • 10
Palmer, Sarah • 10 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
galaxy • 625 views
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modified 7.1 years ago by fubar ♦ 1.1k • written 7.1 years ago by Palmer, Sarah • 10
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7.1 years ago by
fubar ♦ 1.1k
Australia
fubar ♦ 1.1k wrote:
Hi, Sarah. The message you saw: 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? -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
ADD COMMENT • link written 7.1 years ago by fubar ♦ 1.1k
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