Re: [galaxy-dev] Trackster error after upgrade
Hi Jeremy, Thanks for you assistance. I would love to try your suggestions, but Galaxy won't start anymore. I have found the root cause of the problems: my home partition has become too small, due to a fat 'job_working_directory'. I didn't expect it to become so big (especially with tophat output). Now I have the job_working_directory mounted on our network share. So I restart Galaxy, and got this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 85, in __init__ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 84, in __init__ self.load_integrated_tool_panel_keys() File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 236, in load_integrated_tool_panel_keys tree = util.parse_xml( self.integrated_tool_panel_config ) File /home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 584, in parse self._root = parser.close() File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 1251, in close self._parser.Parse(, 1) # end of data ExpatError: unclosed token: line 109, column 4 Removing PID file main.pid Before dragging up my backup, any idea how to fix this otherwise? I suspect that mercurial could not pull all changes in, is that possible? Cheers, Joachim On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote: One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. I've seen this once or twice before but haven't been able to track down the issue yet. Here are two workaround that may help you out: (1) Add the dataset to a new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options -- Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. Best, J. ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
Hi Joachim, It looks like your integrated_tool_panel.xml file has been corrupted somehow. You can move this file to a backup location (or delete) and it should be automatically regenerated on Galaxy startup. If this fixes the issue, could you share a copy of the file? It might be helpful for us to try to figure out what happened to it. Thanks for using Galaxy, Dan On Nov 14, 2012, at 4:25 AM, Joachim Jacob wrote: Hi Jeremy, Thanks for you assistance. I would love to try your suggestions, but Galaxy won't start anymore. I have found the root cause of the problems: my home partition has become too small, due to a fat 'job_working_directory'. I didn't expect it to become so big (especially with tophat output). Now I have the job_working_directory mounted on our network share. So I restart Galaxy, and got this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 85, in __init__ self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 84, in __init__ self.load_integrated_tool_panel_keys() File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line 236, in load_integrated_tool_panel_keys tree = util.parse_xml( self.integrated_tool_panel_config ) File /home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 584, in parse self._root = parser.close() File /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 1251, in close self._parser.Parse(, 1) # end of data ExpatError: unclosed token: line 109, column 4 Removing PID file main.pid Before dragging up my backup, any idea how to fix this otherwise? I suspect that mercurial could not pull all changes in, is that possible? Cheers, Joachim On Wed 14 Nov 2012 04:25:53 AM CET, Jeremy Goecks wrote: One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. I've seen this once or twice before but haven't been able to track down the issue yet. Here are two workaround that may help you out: (1) Add the dataset to a new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options -- Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. Best, J. ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
1) The dist is most recent: [galaxy@galaxy galaxy-dist]$ hg tip changeset: 7982:12fcd068b12e tag: tip user:Daniel Blankenberg d...@bx.psu.edu date:Thu Oct 18 11:22:12 2012 -0400 summary: Do not hide failed datasets with HideDatasetAction post job action. 2) executed [galaxy_home]/static/scripts/pack_scripts.py This solved the problem for all, but one visualisation! One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. URL: http://localhost/visualization/trackster?id=968205d9ed31733d File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 94 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py', line 710 in trackster viz_config = self.get_visualization_config( trans, vis ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line 516 in get_visualization_config tracks.append( pack_track( drawable_dict ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line 467 in pack_track source='data' ) File '/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py', line 94 in get_data_provider data_provider = self.get_data_provider( trans, name=data_provider_name, original_dataset=original_dataset ) File '/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py', line 74 in get_data_provider converted_dataset = original_dataset.get_converted_dataset( trans, name ) File '/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 1152 in get_converted_dataset raise ConverterDependencyException(A dependency (%s) was in an error state. % dependency) ConverterDependencyException: 'A dependency (bgzip) was in an error state.' 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 11/09/2012 08:34 PM, Jeremy Goecks wrote: 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
Re: [galaxy-dev] Trackster error after upgrade
One dataset I want to view in Trackster has an error ConverterDependencyException: 'A dependency (bgzip) was in an error state. I've seen this once or twice before but haven't been able to track down the issue yet. Here are two workaround that may help you out: (1) Add the dataset to a new/saved visualization and then click 'try again' to try reindexing the dataset; (2) copy the dataset using History Options -- Copy Datasets, then delete the failing dataset and try indexing the new dataset. If the dataset continues to fail, please make it available to me and I'll take a look. Best, J. ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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/ ___ 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/
Re: [galaxy-dev] Trackster error after upgrade
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/ ___ 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/
[galaxy-dev] Trackster error after upgrade
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/
Re: [galaxy-dev] Trackster error after upgrade
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/
Re: [galaxy-dev] Trackster error after upgrade
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/
Re: [galaxy-dev] Trackster error after upgrade
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/ ___ 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/
