diff --git a/tools/rgenetics/rgFastQC.py b/tools/rgenetics/rgFastQC.py index 3f828215cca..c2c66bcc844 100644 --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -1,4 +1,7 @@ """ +# added sanitizer for user supplied name +# removed shell and make cl a sequence for Popen call +# ross lazarus August 10 2012 in response to anon insecurity report wrapper for fastqc called as @@ -53,7 +56,7 @@ class FastQC(): cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = re.sub('[^a-zA-Z0-9_]+', '', os.path.basename(self.opts.inputfilename)) + fastqinfilename = re.sub('[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name)