Dannon,

Thank you very much for the help. I will install those dependancies based on the information you sent. Is there any restrictions for path/directory to be installed, for example, should those tools only be installed under ../galaxy-dist/tools?
Thank you!
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