Mercurial > repos > jjohnson > cummerbund
diff cummerbund_wrapper.py @ 8:b0d11fcbc3ac
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 |
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--- a/cummerbund_wrapper.py Wed Oct 10 11:09:15 2012 -0500 +++ b/cummerbund_wrapper.py Thu Oct 11 15:14:51 2012 -0500 @@ -8,13 +8,13 @@ def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) - sys.exit() + sys.exit(1) def html_report_from_directory( html_out, dir ): html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) for fname in sorted( os.listdir( dir ) ): # html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) - html_out.write( '<li><a href="%s"><img src="%s" alt="" height="42" width="42">%s</a></li>\n' % ( fname, fname , fname ) ) + html_out.write( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) ) html_out.write( '</ul>\n</body>\n</html>\n' ) def __main__(): @@ -39,7 +39,7 @@ cmd = ( "Rscript --vanilla %s" % options.r_script ) # Debugging. - print cmd + # print cmd #liubo added, for test, look at the generated R script # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')