⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
Hi Everyone, I was just using my local galaxy instance. I closed it up (from terminal), open IGV to look at some genes, then I restarted it from the terminal and when I tried to access it I got the error message below. I just don't know what happened in these few minutes. Any suggestion how to fix it? Thank you. Luciano URL: http://127.0.0.1:8080/ File '/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/koala2/galaxy-central/lib/galaxy/web/controllers/root.py', line 25 in index m_c=m_c, m_a=m_a ) File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py', line 733 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py', line 744 in fill_template_mako return template.render( **data ) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 691 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 637 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/home/koala2/galaxy-central/database/compiled_templates/root/ index.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/webapps/galaxy/base_panels.mako', _template_uri) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 609 in _inherit_from ret = callable_(template, lclcontext) File '/home/koala2/galaxy-central/database/compiled_templates/webapps/galaxy/ base_panels.mako.py', line 25 in _mako_inherit return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 596 in _inherit_from template = _lookup_template(context, uri, calling_uri) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 626 in _lookup_template return lookup.get_template(uri) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py', line 218 in get_template return self._load(srcfile, uri) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py', line 283 in _load **self.template_args) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 218 in __init__ module = self._compile_from_file(path, filename) File '/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 245 in _compile_from_file module = imp.load_source(self.module_id, path, open(path, 'rb')) IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/ base_panels.mako.py'
On May 10, 2012, at 6:59 PM, Luciano Cosme wrote:
Hi Everyone, I was just using my local galaxy instance. I closed it up (from terminal), open IGV to look at some genes, then I restarted it from the terminal and when I tried to access it I got the error message below. I just don't know what happened in these few minutes. Any suggestion how to fix it? Thank you.
Luciano
...
module = imp.load_source(self.module_id, path, open(path, 'rb')) IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'
Hi Luciano, Could you verify that you started Galaxy as the same user both times? --nate
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Hi, Yes. It is same user and the only used of this system. Thank you. On Fri, May 11, 2012 at 1:33 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On May 10, 2012, at 6:59 PM, Luciano Cosme wrote:
Hi Everyone, I was just using my local galaxy instance. I closed it up (from
terminal), open IGV to look at some genes, then I restarted it from the terminal and when I tried to access it I got the error message below. I just don't know what happened in these few minutes. Any suggestion how to fix it?
Thank you.
Luciano
module = imp.load_source(self.module_id, path, open(path, 'rb')) IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/
... base_panels.mako.py'
Hi Luciano,
Could you verify that you started Galaxy as the same user both times?
--nate
___________________________________________________________ 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:
Hi Luciano, I also ran into the same error after upgrading to the latest build. I found that the following files were owned by root. Not sure how they got changed. galaxyTools/galaxy-central/database/compiled_templates/tool_form.mako.py galaxyTools/galaxy-central/database/compiled_templates/tool_form.mako.pyc After chown and chgrp the files to galaxy, things now are working ok for me again. Give that a try. Cheers, Dave On Mon, May 14, 2012 at 10:12 AM, Luciano Cosme <cosme.simple@gmail.com>wrote:
Hi, Yes. It is same user and the only used of this system. Thank you.
On Fri, May 11, 2012 at 1:33 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On May 10, 2012, at 6:59 PM, Luciano Cosme wrote:
Hi Everyone, I was just using my local galaxy instance. I closed it up (from
terminal), open IGV to look at some genes, then I restarted it from the terminal and when I tried to access it I got the error message below. I just don't know what happened in these few minutes. Any suggestion how to fix it?
Thank you.
Luciano
module = imp.load_source(self.module_id, path, open(path, 'rb')) IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/
... base_panels.mako.py'
Hi Luciano,
Could you verify that you started Galaxy as the same user both times?
--nate
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
-
Dave Lin -
Luciano Cosme -
Nate Coraor