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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