August 2009 - galaxy-user - lists.galaxyproject.org

custom tool output path
by Paul Rigor (prigor＠uci) 04 Aug '09

04 Aug '09

Hi all, For custom tools, I was wondering how the output path can be set in the xml file describing the tool? Are there 'default' variables I should be aware of in order to use as the output path the "user_library_import_dir = database/users" in my universe_wsgi.ini? Thanks, Paul -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor

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error when creating a user
by Paul Rigor (prigor＠uci) 04 Aug '09

04 Aug '09

Hi, Has anyone encountered this error when attempting to create a new user? Thanks, paul URL: http://localhost/user/create File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/debug/prints.py', line 98 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Beaker-0.5-py2.6.egg/beaker/session.py', line 103 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/recursive.py', line 80 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/controllers/user.py', line 178 in create .add_input( "checkbox","Subscribe To Mailing List","subscribe", value='subscribe' ) ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 557 in show_form return self.fill_template( template, form=form, header=header ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 566 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 577 in fill_template_mako return template.render( **data ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/template.py', line 114 in render File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 287 in _render File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 304 in _render_context File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 337 in _exec_template File '/home/prigor/projects/galaxy/genomics/galaxy_dist/database/compiled_templates/ base.mako.py', line 33 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body' -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor

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error even starting up galaxy
by Paul Rigor (prigor＠uci) 04 Aug '09

04 Aug '09

Hi gang, I've setup galaxy to run before. But this time around, the server will not start. The setup is fairly straightforward though I'm using python 2.6. Below is the error message stack. I've made some modifications to the configuration, but just pathing and db stuff. I've even run a python shell to import the new module which works fine. Any suggestions will be really helpful, thanks! Paul Traceback (most recent call last): File "./scripts/paster.py", line 16, in <module> from galaxy import eggs File "/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/__init__.py", line 5, in <module> __import__( "pkg_resources" ).declare_namespace( __name__ ) File "/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/pkg_resources.py", line 16, in <module> import sys, os, zipimport, time, re, imp, new ImportError: No module named new (2.6.2)04:42 PM 16807 prigor@localhost~/projects/galaxy/genomics/galaxy_dist $ python /home/prigor/projects/galaxy/genomics/galaxy_dist/lib/pkg_resources.py -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor

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