Hi Greg - the issue is that when the wrapper processes the Macs output, it attempts to turn the 2nd column of every non-comment line (the "start" field) into an integer (as an aside, it then also subtracts 1 from this value).

Unfortunately the line starting "chr start end ..." isn't commented, so the integer conversion fails causing the error you saw. The patch just traps for the integer conversion error.


HTH, best wishes, Peter

On 27/02/13 19:16, greg wrote:
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



--
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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