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

For dependencies like this, you can usually look at
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies for a few

Good luck,


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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