Dannon,
Thanks and it worked!
Kathryn
________________________________
From: Dannon Baker <dannon.ba...@gmail.com>
To: Kathryn Sun <kathryn....@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....@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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