Hi all,
I tried the latest stable version of Galaxy:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links
to how to use the new tool shed including how to automatically deploy
tools from the shed in a local Galaxy server.
The documentation mentioned some tool shed options available from the
the admin section of Galaxy but I could not locate these options in my
instance of galaxy. So my question is: Can one only take advantage of
the tool deployment from the shed in the development version of Galaxy?
If so, I think the Tool shed wiki should be more clear about this.
Then I tried the latest development version of Galaxy and could locate
the tool shed deployment options. I attempted to install the Grinder
wrapper
(http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp=community&id=3d8312720a69a558&f-deleted=False&show_item_checkboxes=false&async=false&operation=view_or_manage_repository&f-free-text-search=grinder&page=1
<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp=community&id=3d8312720a69a558&f-deleted=False&show_item_checkboxes=false&async=false&operation=view_or_manage_repository&f-free-text-search=grinder&page=1>)
but ran into an error that I am pasting below:
URL:
http://localhost:8080/admin/install_tool_shed_repository?tool_shed_url=toolshed.g2.bx.psu.edu&name=grinder&description=Genomic,%20metagenomic%20and%20amplicon%20read%20simulator&repository_clone_url=http://fan...@toolshed.g2.bx.psu.edu/repos/fangly/grinder&changeset_revision=5ba7c9ac056a
File
'/home/floflooo_mint/Software/galaxy-central/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/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File
'/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File
'/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 173 in decorator
return func( self, trans, *args, **kwargs )
File
'/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/controllers/admin.py',
line 805 in install_tool_shed_repository
shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip(
'./' )
IndexError: list index out of range
I get the same problem with other wrappers such as FastQC. Am I doing
something wrong?
Thanks,
Florent
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