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