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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