Question: Problem visualising Krona pie chart within local Galaxy instance
0
gravatar for fmroche
12 months ago by
fmroche0
fmroche0 wrote:

Hi there,

I have a local instance of the latest version of Galaxy running (17.05).

I'm interested in getting into metagenomics so have installed the tools (MetaPhlAn2 and Krona pie chart) that we used at the Galaxy metagenomics training session in Montpellier. I successfully ran a MetaPhlAn2 analysis and formatted it for Krona, however I'm having problems visualising the html output file from Krona. I get the following message:

Internal Server Error. Galaxy was unable to successfully complete your request

I can download the html file from Galaxy and open it locally no problem at all so the problem is not with the file. Also I've no problem visualising other html files in Galaxy such as the output from FastQC.

When I check the paster.log file this is the error reported:

Error - <class 'sgmllib.sgmlparseerror'="">: unexpected u'\\' char in declaration URL: http://X.X.X.X:8080/datasets/b701da857886499b/display/?preview=True File '/home/lab/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/home/lab/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/home/lab/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/home/lab/galaxy/lib/galaxy/web/framework/base.py', line 135 in __call__ return self.handle_request( environ, start_response ) File '/home/lab/galaxy/lib/galaxy/web/framework/base.py', line 214 in handle_request body = method( trans, *kwargs ) File '/home/lab/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 252 in display return data.datatype.display_data(trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, *kwd) File '/home/lab/galaxy/lib/galaxy/datatypes/data.py', line 382 in display_data return sanitize_html(open( data.file_name ).read()).encode('utf-8') File '/home/lab/galaxy/lib/galaxy/util/sanitize_html.py', line 438 in sanitize_html p.feed(unicodify(htmlSource, encoding)) File '/home/lab/galaxy/lib/galaxy/util/sanitize_html.py', line 92 in feed sgmllib.SGMLParser.feed(self, data) File '/usr/lib/python2.7/sgmllib.py', line 104 in feed self.goahead(0) File '/usr/lib/python2.7/sgmllib.py', line 174 in goahead k = self.parse_declaration(i) File '/usr/lib/python2.7/markupbase.py', line 140 in parse_declaration "unexpected %r char in declaration" % rawdata[j]) File '/usr/lib/python2.7/sgmllib.py', line 111 in error raise SGMLParseError(message) SGMLParseError: unexpected u'\\' char in declaration

Any ideas would be very much appreciated!!

Thanks,

Fiona

krona html metagenomics • 259 views
ADD COMMENTlink modified 11 months ago • written 12 months ago by fmroche0
0
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is using the latest Krona tool version (2.6.1), correct? Has Krona been added to the whitelist under Admin > Manage Display Whitelist. If you do add it, does that correct the display?

If that does not resolve the problem, the administrator of the instance may be able to help, or if you are the admin, share more details and we can try to help troubleshoot more.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 11 months ago • written 12 months ago by Jennifer Hillman Jackson25k
0
gravatar for fmroche
11 months ago by
fmroche0
fmroche0 wrote:

Thanks a million Jen, that fixed it!

ADD COMMENTlink written 11 months ago by fmroche0
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