Hi Kathryn, It looks like you haven't installed FastQC (or potentially installed it and just haven't made it accessible to Galaxy). You'll need to install FastQC from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ if you haven't already, and the main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc.
For dependencies like this, you can usually look at http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies for a few pointers. Good luck, Dannon On Thu, May 9, 2013 at 9:43 AM, Kathryn Sun <kathryn....@ymail.com> wrote: > Dannon, > > I've set up galaxy at the local linux. After data configuration, I run > fastqc to check how it runs. Here I got error message as below -- > > error > An error occurred running this job: Traceback (most recent call last): > File "../galaxy-dist/tools/rgenetics/rgFastQC.py", line 158, in assert > os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find > executable %s' % opts.executable AssertionError: ##r > > Here is the detail of the error -- > Tool: FastQC:Read QC > Name: FastQC_FASTQ Groomer on data 6.html > Created: May 02, 2013 > Filesize: 0 bytes > Dbkey: mm9 > Format: html > Tool Version: > Tool Standard Output: stdout > Tool Standard Error: stderr > Tool Exit Code: 1 > > Input Parameter Value > Short read data from your current history 8: FASTQ Groomer on data 6 > Title for the output file - to remind you what the job was for FastQC > Contaminant list No dataset > > What might be the problem? Thank you! > Kathryn > > >
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