Question: Ipython on local galaxy
1
gravatar for cristianrohr768
2.3 years ago by
cristianrohr76820 wrote:

Hello,

i have a local installation of galaxy on a ubuntu 16.04 64 bits

I try to run the iPython visualization, but get this error:

127.0.0.1 - - [14/jul/2016:12:35:48 -0300] "GET /api/histories/0a248a1f62a0cc04/contents/datasets/81991b32733a4fc4 HTTP/1.1" 200 - "http://localhost:8081/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.106 Safari/537.36" galaxy.webapps.galaxy.controllers.visualization ERROR 2016-07-14 12:35:51,527 error rendering visualization (ipython): 'Undefined' object has no attribute 'endswith' Traceback (most recent call last): File "/home/horus/software/galaxy/lib/galaxy/webapps/galaxy/controllers/visualization.py", line 750, in render return plugin.render( trans=trans, embedded=embedded, *kwargs ) File "/home/horus/software/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 135, in render return self._render( render_vars, trans=trans, embedded=embedded ) File "/home/horus/software/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 234, in _render return trans.fill_template( template_filename, template_lookup=self.template_lookup, *render_vars ) File "/home/horus/software/galaxy/lib/galaxy/web/framework/webapp.py", line 858, in fill_template return self.fill_template_mako( filename, *kwargs ) File "/home/horus/software/galaxy/lib/galaxy/web/framework/webapp.py", line 872, in fill_template_mako return template.render( *data ) File "/home/horus/software/galaxy/.venv/lib/python2.7/site-packages/mako/template.py", line 445, in render return runtime._render(self, self.callable_, args, data) File "/home/horus/software/galaxy/.venv/lib/python2.7/site-packages/mako/runtime.py", line 829, in _render *_kwargs_for_callable(callable_, data)) File "/home/horus/software/galaxy/.venv/lib/python2.7/site-packages/mako/runtime.py", line 864, in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File "/home/horus/software/galaxy/.venv/lib/python2.7/site-packages/mako/runtime.py", line 890, in _exec_template callable_(context, *args, *kwargs) File "/home/horus/software/galaxy/database/compiled_templates/ipython.mako.py", line 42, in render_body ie.set_id("ipython") File "/home/horus/software/galaxy/database/compiled_templates/ie.mako.py", line 356, in render_set_id self.attr.our_config_dir = os.path.join(plugin_path, "config") File "/home/horus/software/galaxy/.venv/lib/python2.7/posixpath.py", line 70, in join elif path == '' or path.endswith('/'): AttributeError: 'Undefined' object has no attribute 'endswith'

any help?

ipython • 753 views
ADD COMMENTlink written 2.3 years ago by cristianrohr76820
1
gravatar for Bjoern Gruening
2.3 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Can you please make sure you have the latest updates fro 16.04? Make also sure you are using the Jupyter interactive environment. The IPython one is deprecated.

ADD COMMENTlink written 2.3 years ago by Bjoern Gruening5.1k
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