commit/galaxy-central: fubar: better tool naming in outputs for all picard tools and finally found where the picard log was hiding - galaxy-commits

8 May 2011

1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/1497b1668510/
changeset:   r5517:1497b1668510
user:        fubar
date:        2011-05-09 04:16:18
summary:     better tool naming in outputs for all picard tools and finally found where the picard log was hiding
affected #:  1 file (21 bytes)

--- a/tools/picard/picard_wrapper.py	Sun May 08 21:21:51 2011 -0400
+++ b/tools/picard/picard_wrapper.py	Sun May 08 22:16:18 2011 -0400
@@ -22,7 +22,7 @@
 <body><div class="document">
 """
-galhtmlattr = """Galaxy tool wrapper run %s at %s</b><br/>"""
+galhtmlattr = """Galaxy tool wrapper %s at %s</b><br/>"""
 galhtmlpostfix = """</div></body></html>\n"""
@@ -68,7 +68,7 @@
             os.makedirs(opts.tmpdir)
         except:
             pass
-        self.log_filename = '%s.log' % self.picname
+        self.log_filename = os.path.join(opts.outdir,'%s.log' % self.picname)
         self.metricsOut =  os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
def baseName(self,name=None):
@@ -237,7 +237,7 @@
         tr.d1 td {background-color: aliceblue; color: black;}
         </style>"""    
         res = [rstyle,]
-        res.append(galhtmlprefix % self.progname)   
+        res.append(galhtmlprefix % self.picname)   
         res.append(galhtmlattr % (self.progname,timenow()))
         flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')] 
         pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.

    