David,
The reason shed_tools should be outside the Galaxy path is that tool
shed mercurial repositories can interfere with the Galaxy mercurial
repository, since mercurial will find more than one .hg directory. As
long as the data you want to store is not a mercurial repository, you
should be safe, but my advice would still be to locate it outside the
Galaxy path to avoid any possibility of conflicts.
--Dave B.
On 4/16/13 16:28:01.000, David Bonsall wrote:
Thanks Dave
A quick update from /galaxy-dist ....
% hg update stable
.....did the trick!
Btw, I have another question I have since added sub-directories to /galaxy-dist
to store blast databases etc. Is this bad? Will mercurial be able to update. I
remember a warning to not install shed-tools directory in the main galaxy stem
for this reason. Does this rule apply to all directories?
Best Wishes
David
On Tue, Apr 16, 2013 at 9:16 PM, Dave Bouvier <d...@bx.psu.edu
<mailto:d...@bx.psu.edu>> wrote:
David,
Thank you for reporting this error, which was due to a new tool shed
feature being introduced in -central, which had not yet been wrapped
in a backwards compatibility layer for -dist. As of
9440:bbb229927c68, the issue should be resolved.
--Dave B.
On 4/11/13 12:51:03.000, David Bonsall wrote:
Dear Galaxy team,
I'm trying to install NCBI + tools on a local instance of galaxy
(rep:
8.1546099212f), but I get the following error, which I do not
get when
trying to install other tools.
Thank you for all your hard work. It's all much appreciated
David
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ HTTPError: HTTP Error 500: Internal Server Error
URL:
http://127.0.0.1:8080/admin___toolshed/prepare_for_install?__tool_shed_url=http://toolshed.__g2.bx.psu.edu/&repository_ids=__1d92ebdf7e8d466c&changeset___revisions=1f546099212f
<http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=1f546099212f>
Module weberror.evalexception.__middleware:364 in respond
view
>> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:125 in __call__ view
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:182 in handle_request view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:228 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.__controllers.admin_toolshed:894 in
prepare_for_install view
>> common_install_util.get___dependencies_for_repository( trans,
tool_shed_url, repo_info_dict, includes_tool_dependencies )
Module tool_shed.util.common_install___util:90 in
get_dependencies_for___repository view
>> required_repo_info_dicts = get_required_repo_info_dicts(
tool_shed_url, util.listify( repo_info_dict ) )
Module tool_shed.util.common_install___util:283 in
get_required_repo_info_dicts view
>> response = urllib2.urlopen( url )
Module urllib2:126 in urlopen view
>> return _opener.open(url, data, timeout)
Module urllib2:400 in open view
>> response = meth(req, response)
Module urllib2:513 in http_response view
>> 'http', request, response, code, msg, hdrs)
Module urllib2:438 in error view
>> return self._call_chain(*args)
Module urllib2:372 in _call_chain view
>> result = func(*args)
Module urllib2:521 in http_error_default view
>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
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___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
