Hello Matthias,

The setting for tool_path is likely not the culprit. Your success in being able to install the repository is most likely due to the small fix I committed to the tool shed yesterday afternoon that affected the contents of this particular tool suite.

You should be running the tip of the Galaxy central repository which is currently 7334:951ba799c0b0 in order to use the public tool sheds with your local Galaxy instance. I've made significant changes recently with installing tool shed repositories, so you may bump into additional issues if you're not running the tip.

I think that based on your revision, you do not yet have 2 new columns in the tool_shed_repository table of your local Galaxy instance's database. But just to be sure, does your tool_shed_repository table have a status and an error_message column? If you don't, thats actually ok because the "steps" I was referring to in my previous email are not necessary, but you should still update your Galaxy to the tip asap.

Thanks Matthias!

Greg Von Kuster

On Jul 3, 2012, at 5:23 AM, Hollander, Mattias de wrote:

Hi Greg,

1. changeset: 7284:87be4c8d7f7f

2. <toolbox tool_path="./shed_tools">

3. yes, the latest

Solved! I noticed that my tool_path was different from yours. After setting it to ../shed_tools it installed correctly.

Thanks!

On 07/02/2012 09:41 PM, Greg Von Kuster wrote:

...

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=h... 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!

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