This tool has been stable for a while now and that variable cl is defined
as a list in line 52 just above line 63, so this error seems very strange
unless you made changes to the source code?
It's hard to know where to start helping because there are lots of useful
pieces of information you have not yet provided - at the very least, please
always provide the version of Galaxy source (the output of hg heads will
help) and python you are running.
Just to check that the source is as it should be, can you please try:
hg diff tools/rgenetics/rgFastQC.py
hg diff tools/rgenetics/rgFastQC.xml
from your Galaxy root - if you get any output, try
hg revert tools/rgenetics/rgFastQC.py
hg revert tools/rgenetics/rgFastQC.xml
and then try running it again?
On Thu, Feb 21, 2013 at 6:46 AM, Min Cho <m...@ba-lab.com> wrote:
> When trying to run FastQC, I get this error:
> Traceback (most recent call last):
> File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 162, in
> html,retval,serr = f.run_fastqc()
> File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 63, in
> sout.write('# FastQC cl = \n' % ' '.join(cl))
> TypeError: not all arguments converted during string formatting
> Is there anything I can do to modify the code to fix this? I'm using data
> run through FASTQ Groomer.
> Thank you****
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