Question: Error in running jupyter on galaxy in local system
0
gravatar for sabu.george
16 days ago by
sabu.george0 wrote:

I am trying to run ipython notebook with the locally installed galaxy. I went through the following document to set this up. I am getting the following error:

galaxy.webapps.galaxy.controllers.visualization ERROR 2018-01-02 18:20:55,516 error rendering visualization (jupyter) Traceback (most recent call last): File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/visualization.py", line 673, in render return plugin.render(trans=trans, embedded=embedded, kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 135, in render return self._render(render_vars, trans=trans, embedded=embedded) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 290, in _render return trans.fill_template(template_filename, template_lookup=self.template_lookup, *render_vars) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/web/framework/webapp.py", line 916, in fill_template return self.fill_template_mako(filename, *kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/web/framework/webapp.py", line 930, in fill_template_mako return template.render(data) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py", line 445, in render return runtime._render(self, self.callable_, args, data) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 829, in _render *_kwargs_for_callable(callable_, data)) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 864, in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 890, in _exec_template callable_(context, *args, *kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/database/compiled_templates/jupyter.mako.py", line 89, in render_body __M_writer(unicode( ie.default_javascript_variables() )) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/database/compiled_templates/ie.mako.py", line 122, in render_default_javascript_variables __M_writer(unicode( self.javascript_boolean(self.attr.PASSWORD_AUTH) )) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 356, in __getattr__ raise AttributeError(key) AttributeError: PASSWORD_AUTH

I tried hardcoding these values in place of variables by getting the value from the file lib/galaxy/web/base/interactive_environments.py with print statements. Then I am getting the following error.

galaxy.webapps.galaxy.controllers.visualization ERROR 2018-01-02 16:56:32,282 error rendering visualization (jupyter) Traceback (most recent call last): File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/visualization.py", line 673, in render return plugin.render(trans=trans, embedded=embedded, kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 135, in render return self._render(render_vars, trans=trans, embedded=embedded) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 290, in _render return trans.fill_template(template_filename, template_lookup=self.template_lookup, *render_vars) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/web/framework/webapp.py", line 916, in fill_template return self.fill_template_mako(filename, *kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/lib/galaxy/web/framework/webapp.py", line 930, in fill_template_mako return template.render(data) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py", line 445, in render return runtime._render(self, self.callable_, args, data) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 829, in _render *_kwargs_for_callable(callable_, data)) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 864, in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 890, in _exec_template callable_(context, *args, *kwargs) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/database/compiled_templates/jupyter.mako.py", line 95, in render_body __M_writer(unicode( ie.plugin_require_config() )) File "/home/elucidata/elucidata/MITU/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py", line 625, in __getattr__ self.name, key)) AttributeError: Namespace 'ie' has no member 'plugin_require_config'

Please help me solve this issue. Thanks.

ADD COMMENTlink modified 15 days ago • written 16 days ago by sabu.george0
0
gravatar for sabu.george
15 days ago by
sabu.george0 wrote:

The problem got solved somehow. Did a fresh installation of the galaxy on a fresh machine and everything worked fine.

ADD COMMENTlink written 15 days ago by sabu.george0
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