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comparison cummerbund_wrapper.py @ 8:b0d11fcbc3ac

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cummerbund add MDS and PCA plots, handle errors from R
author Jim Johnson <jj@umn.edu>
date Thu, 11 Oct 2012 15:14:51 -0500
parents 6a9bc26ab8d9
children 2d7eee38ab5b
comparison
equal deleted inserted replaced
7:c2b922c9d545 8:b0d11fcbc3ac
6 6
7 import optparse, os, shutil, subprocess, sys, tempfile 7 import optparse, os, shutil, subprocess, sys, tempfile
8 8
9 def stop_err( msg ): 9 def stop_err( msg ):
10 sys.stderr.write( "%s\n" % msg ) 10 sys.stderr.write( "%s\n" % msg )
11 sys.exit() 11 sys.exit(1)
12 12
13 def html_report_from_directory( html_out, dir ): 13 def html_report_from_directory( html_out, dir ):
14 html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) 14 html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
15 for fname in sorted( os.listdir( dir ) ): 15 for fname in sorted( os.listdir( dir ) ):
16 # html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) 16 # html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
17 html_out.write( '<li><a href="%s"><img src="%s" alt="" height="42" width="42">%s</a></li>\n' % ( fname, fname , fname ) ) 17 html_out.write( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) )
18 html_out.write( '</ul>\n</body>\n</html>\n' ) 18 html_out.write( '</ul>\n</body>\n</html>\n' )
19 19
20 def __main__(): 20 def __main__():
21 #Parse Command Line 21 #Parse Command Line
22 parser = optparse.OptionParser() 22 parser = optparse.OptionParser()
37 37
38 # Build command. 38 # Build command.
39 cmd = ( "Rscript --vanilla %s" % options.r_script ) 39 cmd = ( "Rscript --vanilla %s" % options.r_script )
40 40
41 # Debugging. 41 # Debugging.
42 print cmd 42 # print cmd
43 43
44 #liubo added, for test, look at the generated R script 44 #liubo added, for test, look at the generated R script
45 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script') 45 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
46 46
47 47