--- a/rgGSEA/rgGSEA.py	Sun Jun 09 02:06:52 2013 -0400
+++ b/rgGSEA/rgGSEA.py	Sun Jun 09 23:09:34 2013 -0400
@@ -161,7 +161,8 @@
                 print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir)
                 sys.exit(1)
         fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report
-        fakeGMT = os.path.join(opts.output_dir,fakeGMT) 
+        fakeGMT = os.path.join(opts.output_dir,fakeGMT)
+        fakeGMT = os.path.abspath(fakeGMT)
         fakeRanks = '%s.rnk' % fakeGMT
         if not fakeGMT.endswith('.gmt'):
             fakeGMT = '%s.gmt' % fakeGMT
@@ -323,6 +324,7 @@
         if len(ranks) < 2:
              print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname
              sys.exit(1)
+        print '### opening %s and writing %s' % (fakeRanks,str(ranks[:10]))
         rclean = open(fakeRanks,'w')
         rclean.write('contig\tscore\n')
         rclean.write('\n'.join(ranks))