Dannon, Thanks and it worked! Kathryn ________________________________ From: Dannon Baker <dannon.baker@gmail.com> To: Kathryn Sun <kathryn.sun@ymail.com> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Sent: Friday, May 10, 2013 10:07 AM Subject: Re: Error with fastqc 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