--- a/FastQC/rgFastQC.py	Tue Jun 04 22:18:27 2013 -0400
+++ b/FastQC/rgFastQC.py	Tue Jun 04 22:42:51 2013 -0400
@@ -27,6 +27,25 @@
 import zipfile
 import gzip
 
+def pathfind(program):
+    """ toolshed path munging isn't so try to work around june 5 2013
+    """
+    def is_exe(fpath):
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            path = path.strip('"')
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+
+    return None    
+
 class FastQC():
     """wrapper
     """
@@ -35,6 +54,9 @@
     def __init__(self,opts=None):
         assert opts <> None
         self.opts = opts
+        fastqcexe = pathfind(opts.executable)
+        assert (fastqcexe != None),'##rgFastQC.py error - cannot find passed fastqc executable %s in path %s' % (opts.executable,os.environ['PATH'])
+        self.fastqcexe = fastqcexe
         
     def getFileString(self, fpath, outpath):
         """
@@ -68,7 +90,7 @@
         dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
         sout = open(tlog, 'w')
         fastq = os.path.basename(self.opts.input)
-        cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir]
+        cl = [self.fastqcexe,'--outdir=%s' % self.opts.outputdir]
         if self.opts.informat in ['sam','bam']:
             cl.append('--f=%s' % self.opts.informat)
         if self.opts.contaminants <> None :
@@ -184,7 +206,6 @@
                        shutil.move(sauce,dest)
                 os.rmdir(adir)
 
-    
 
 if __name__ == '__main__':
     op = optparse.OptionParser()
@@ -198,7 +219,6 @@
     op.add_option('-e', '--executable', default='fastqc')
     opts, args = op.parse_args()
     assert opts.input <> None
-    assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
     if not os.path.exists(opts.outputdir): 
         os.makedirs(opts.outputdir)
     f = FastQC(opts)