Can you please verify that you're running the most recent dist? In the most recent dist, requireJS modules are used, so Dataset is prefixed with its module, e.g.
https://bitbucket.org/galaxy/galaxy-dist/src/12fcd068b12eb844d7eded11bd70826c4275021c/static/scripts/viz/visualization.js?at=default#cl-726 However, the errors you're reporting indicate no module is used. Another thing to try: repacking/reminifying the JavaScript files: % cd <galaxy_home>/static/scripts % python pack_scripts.py If that still doesn't work, you could try commenting out the apache rewrite rule for packed scripts and see if that solves the problem. If so, then the problem is narrowed down to the packed scripts, one way or another. J. On Nov 9, 2012, at 12:37 AM, Joachim Jacob wrote: > Thanks for your suggestion, Hans-Rudolf. Unfortunately, no success. > Looking into it bit deeper. Keep suggestions coming ;-) > > Joachim > > On 11/08/2012 05:00 PM, Hans-Rudolf Hotz wrote: >> Hi Joachim >> >> This might be completely unrelated, but your situation reminds me of our >> case when we did the last update (to "Oct 5th release"): >> >> All previously stored visualizations didn't work any more a first. I had to >> modify the datatypes_conf.xml file by adding >> >> the following line: >> >> <datatype extension="fli" >> type="galaxy.datatypes.tabular:FeatureLocationIndex" >> display_in_upload="false"/> >> >> >> and add >> <converter file="bed_to_fli_converter.xml" target_datatype="fli"/> >> >> and <converter file="gff_to_fli_converter.xml" target_datatype="fli"/> >> >> to the bed and gff definitions, respectively. >> >> (the differences are easy to spot when you compare your 'datatypes_conf.xml' >> file with the new 'datatypes_conf.xml.sample' file.) >> >> >> After making the changes and restarting the server, the saved visualization >> were re-indexed as soon as I tried to open them, but finally, the were >> visible again. >> >> >> Regards, Hans-Rudolf >> >> >> On 11/08/2012 04:21 PM, Joachim Jacob wrote: >>> Clearing cache did not solve it. >>> >>> The Js console reports (when trying to visualize an short-read alignment): >>> >>> Uncaught ReferenceError: Dataset is not defined visualization.js:1 >>> Uncaught ReferenceError: Dataset is not defined tracks.js:1 >>> Uncaught ReferenceError: Dataset is not defined tracks.js:1 >>> >>> >>> Thanks, >>> Joachim >>> >>> Joachim Jacob, PhD >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> On 11/08/2012 04:14 PM, Jeremy Goecks wrote: >>>> Try clearing your browser cache and see if that does the trick. >>>> >>>> If not, please open your JavaScript console and report the errors that >>>> you're seeing. >>>> >>>> Thanks, >>>> J. >>>> >>>> On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote: >>>> >>>>> Hi all, >>>>> >>>>> After upgrading to the latest galaxy-dist, Trackster does not behave. >>>>> >>>>> Nearly all saved viz's just show a blank main window, while just >>>>> displaying the Galaxy header and the trackster header bar. >>>>> >>>>> In contrast, one visualisation gives this error: >>>>> ConverterDependencyException: 'A dependency (bgzip) was in an error >>>>> state.' >>>>> >>>>> Any help appreciated, thanks. >>>>> >>>>> Joachim >>>>> >>>>> -- >>>>> Joachim Jacob, PhD >>>>> >>>>> Rijvisschestraat 120, 9052 Zwijnaarde >>>>> Tel: +32 9 244.66.34 >>>>> Bioinformatics Training and Services (BITS) >>>>> http://www.bits.vib.be >>>>> @bitsatvib >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> >>>>> http://lists.bx.psu.edu/ >>>> >>>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >
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