Thanks Peter.  I'm running it now after applying your fix.

Any idea what the problem was?

-Greg

On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> Hello Greg
>
> It looks like you're running the version of the MACS14 tool from the
> toolshed? I think we also ran into this here and I patched the
> macs14_wrapper.py thusly to work around it:
>
> diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py
> index ccefb10..c0cf099 100644
> --- a/macs14/macs142_wrapper.py
> +++ b/macs14/macs142_wrapper.py
> @@ -37,7 +37,13 @@ def xls_to_interval( xls_file, interval_file, header =
> None ):
>          else:
>              fields = line.split( '\t' )
>              if len( fields ) > 1:
> -                fields[1] = str( int( fields[1] ) - 1 )
> +                try:
> +                    # Try to convert 'start' to int and shift
> +                    fields[1] = str( int( fields[1] ) - 1 )
> +                except ValueError:
> +                    # Integer conversion failed so comment out
> +                    # "bad" line instead
> +                    fields[0] = "#%s" % fields[0]
>              out.write( '\t'.join( fields ) )
>      out.close()
>
> I'm intending to feed this back to the tool authors once things got a bit
> quieter here.
>
> HTH, best wishes
>
> Peter
>
>
> On 26/02/13 15:52, greg wrote:
>>
>> Hi guys,
>>
>> (Sorry for showing up on this list so much, hopefully I'll get
>> everything running soon!)
>>
>>
>> On our local galaxy install when I try to run MACS14 like this:
>> http://snag.gy/RYBBN.jpg
>>
>> we get this error:
>>
>> Dataset generation errors
>>
>> Dataset 74: MACS14 on data 29 and data 24 (peaks: bed)
>>
>> Tool execution generated the following error message:
>>
>> Traceback (most recent call last):
>>    File
>> "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py",
>> line 132, in <module>
>>      if __name__ == "__main__": main()
>>    File
>> "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py",
>> line 94, in main
>>      xls_to_interval( create_peak_xls_file,
>> options['xls_to_interval']['peaks_file'], header = 'peaks file' )
>>    File
>> "/misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py",
>> line 40, in xls_to_interval
>>      fields[1] = str( int( fields[1] ) - 1 )
>> ValueError: invalid literal for int() with base 10: 'start'
>> ___________________________________________________________
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>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
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