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.sun@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