Hello Matthias, I've just updated the tool shed to changeset revision 7332:e54f7684c919 and I've successfully installed the mothur toolsuite. This revision includes a fix that may be related to the issue you encountered. However, before you try reinstalling, can you reply with answers to each of the following? This will help me know what steps you'll need to take before attempting the installation. I'll reply back with what steps you should take as soon as I hear from you.
1. What changeset revision are you running on your Galaxy instance? 2. What is the setting for tool_path in your shed_tool_conf.xml file - is it the default of ../shed_tools ? 3. What changeset revision of the mothur tool suite were you trying to install - is the the tip of 5c77423823cb in the main tool shed? Thanks! Greg Von Kuster On Jul 2, 2012, at 10:57 AM, Hollander, Mattias de wrote: > Hi, > > I am trying to install the mothur toolsuite via the toolshed but this > returns in an HTTP 500 error: > > URL: > http://galaxy.nioo.knaw.nl/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&install_tool_dependencies=&repo_info_dict=ea2e290f2209f91ca1303230f6223b698a53945f%3A7b226d6f746875725f746f6f6c7375697465223a205b224d6f74687572206d65746167656e6f6d69637320636f6d6d616e64732061732047616c61787920746f6f6c73222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6a6a6f686e736f6e2f6d6f746875725f746f6f6c7375697465222c2022323964623862363138346561222c20223130225d7d&includes_tools=True > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', > > line 144 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', > > line 106 in __call__ > environ, self.app) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', > > line 543 in intercept_output > app_iter = application(environ, replacement_start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > > line 84 in __call__ > return self.application(environ, start_response) > File > '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > > line 633 in __call__ > return self.application(environ, start_response) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', > line 160 in __call__ > body = method( trans, **kwargs ) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', > line 184 in decorator > return func( self, trans, *args, **kwargs ) > File > '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', > > line 451 in install_repository > clone_repository( repository_clone_url, os.path.abspath( > relative_install_dir ), ctx_rev ) > File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', > line 286 in clone_repository > rev=[ ctx_rev ] ) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/commands.py', > > line 1157 in clone > branch=opts.get('branch')) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/hg.py', > > line 350 in clone > destrepo.clone(srcrepo, heads=revs, stream=stream) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/localrepo.py', > > line 2280 in clone > return self.pull(remote, heads) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/localrepo.py', > > line 1582 in pull > remotephases = remote.listkeys('phases') > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/wireproto.py', > > line 115 in plain > encresref.set(self._submitone(f.func_name, encargsorres)) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/wireproto.py', > > line 163 in _submitone > return self._call(op, **args) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/httprepo.py', > > line 169 in _call > fp = self._callstream(cmd, **args) > File > '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/httprepo.py', > > line 117 in _callstream > resp = self.urlopener.open(req) > File '/usr/lib/python2.7/urllib2.py', line 397 in open > response = meth(req, response) > File '/usr/lib/python2.7/urllib2.py', line 510 in http_response > 'http', request, response, code, msg, hdrs) > File '/usr/lib/python2.7/urllib2.py', line 435 in error > return self._call_chain(*args) > File '/usr/lib/python2.7/urllib2.py', line 369 in _call_chain > result = func(*args) > File '/usr/lib/python2.7/urllib2.py', line 518 in http_error_default > raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) > HTTPError: HTTP Error 500: Internal Server Error > > Any ideas how to fix this? > > Thanks! ___________________________________________________________ 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: http://lists.bx.psu.edu/
