| Previous changeset 3:d75fd880fce2 (2015-01-11) Next changeset 5:e9c858c8aa6e (2015-01-11) |
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Commit message:
Uploaded |
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modified:
rgToolFactory2.py |
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added:
savedeps.xml |
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| diff -r d75fd880fce2 -r b85a3b92e9f7 rgToolFactory2.py --- a/rgToolFactory2.py Sun Jan 11 22:01:27 2015 -0500 +++ b/rgToolFactory2.py Sun Jan 11 23:03:00 2015 -0500 |
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| @@ -190,15 +190,15 @@ self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later self.pyfile = self.myname # crude but efficient - the cruft won't hurt much self.xmlfile = '%s.xml' % self.toolname - s = open(self.opts.script_path,'r').readlines() - s = [x.rstrip() for x in s] # remove pesky dos line endings if needed - self.script = '\n'.join(s) + rx = open(self.opts.script_path,'r').readlines() + rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed + self.script = '\n'.join(rx) fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) tscript = open(self.sfile,'w') # use self.sfile as script source for Popen tscript.write(self.script) tscript.close() - self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help - self.escapedScript = '\n'.join([html_escape(x) for x in s]) + self.indentedScript = "<![CDATA[%s]]>" % '\n'.join([' %s' % x for x in rx]) # for restructured text in help + self.escapedScript = "<![CDATA[%s]]>" % self.script) self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname) if opts.output_dir: # may not want these complexities self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) |
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| diff -r d75fd880fce2 -r b85a3b92e9f7 savedeps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/savedeps.xml Sun Jan 11 23:03:00 2015 -0500 |
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| @@ -0,0 +1,18 @@ +x +xmlgoeshereBiocGenerics_0.8.0.tar.gz?raw=true</package> +xmlgoeshereIRanges_1.20.7.tar.gz?raw=true</package> +xmlgoeshereXVector_0.2.0.tar.gz?raw=true</package> +xmlgoeshereGenomicRanges_1.14.4.tar.gz?raw=true</package> +xmlgoeshereRcpp_0.11.3.tar.gz?raw=true</package> +xmlgoeshereRcppArmadillo_0.4.600.0.tar.gz?raw=true</package> +xmlgoesherelocfit_1.5-9.1.tar.gz?raw=true</package> +xmlgoeshereBiobase_2.22.0.tar.gz?raw=true</package> +xmlgoeshereDBI_0.3.1.tar.gz?raw=true</package> +xmlgoeshereRSQLite_1.0.0.tar.gz?raw=true</package> +xmlgoeshereAnnotationDbi_1.24.0.tar.gz?raw=true</package> +xmlgoesherextable_1.7-4.tar.gz?raw=true</package> +xmlgoeshereXML_3.98-1.1.tar.gz?raw=true</package> +xmlgoeshereannotate_1.40.1.tar.gz?raw=true</package> +xmlgoesheregenefilter_1.44.0.tar.gz?raw=true</package> +xmlgoeshereRColorBrewer_1.1-2.tar.gz?raw=true</package> +xmlgoeshereDESeq2_1.2.10.tar.gz?raw=true</package> |