Perhaps these are the files that have conflicts. You'll have to get someone local that can determine the problems with your environment that are not allowing you to get clean updates to your Galaxy code. On Jan 29, 2013, at 10:11 AM, Waldron, Michael H wrote:
Not that I know of. We have only edited configuration files and .loc files for various tools.
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, January 29, 2013 10:07 AM To: Waldron, Michael H Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
Have you made some changes to your local Galaxy code base that require merging?
On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote:
To be honest, I barely understand this enough to just follow the wiki instructions. When it doesn't work as expected, I'm lost.
I did go back to the output from when I ran the update, and just noticed something about not updating because of new heads. What does this mean?
[galaxy@galaxy galaxy-dist]$ hg pull -u pulling from https://bitbucket.org/galaxy/galaxy-central searching for changes adding changesets adding manifests adding file changes added 691 changesets with 2002 changes to 603 files (+1 heads) not updating, since new heads added (run 'hg heads' to see heads, 'hg merge' to merge)
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:52 AM To: Waldron, Michael H Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
Hi Michael,
Your paster log still is showing the older code. Any idea how this happens in your environment?
On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:
I had stopped the Galaxy server before running the update, then started it afterward.
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:12 AM To: Waldron, Michael H Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
Hi Michael,
Did you restart your Galaxy server after updating from Galaxy central? Your paster log shows the following:
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
However, that line no longer exists in the revision to which you've updated, and line 1201 of the admin_toolshed.py file is now:
status = kwd.get( 'status', 'done' )
Greg Von Kuster
On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:
Here is the output from hg heads.
[galaxy@galaxy galaxy-dist]$ hg heads changeset: 8677:22788c1262a2 tag: tip user: jeremy goecks <jeremy.goecks@emory.edu> date: Mon Jan 28 16:36:02 2013 -0500 summary: Language improvements for tophat wrappers.
changeset: 7987:966a9b393b85 branch: add_requirement_tags_for_plink parent: 7472:06b31a61793c user: Dannon Baker <dannonbaker@me.com> date: Mon Aug 13 13:23:54 2012 -0400 summary: Branch close
changeset: 7152:ffc20445b35e branch: split_blast2 parent: 7058:22f545c0d412 user: Dannon Baker <dannonbaker@me.com> date: Wed Apr 18 07:59:38 2012 -0400 summary: Branch close.
changeset: 7151:c94957ac5454 branch: workflow_import_menu_api parent: 6834:1a3d01b09f7a user: Dannon Baker <dannonbaker@me.com> date: Wed Mar 21 09:50:44 2012 -0400 summary: Branch close for pull request.
changeset: 7150:314a10ae112d branch: split_blast parent: 6757:ebf65c0b1e26 user: Dannon Baker <dannonbaker@me.com> date: Tue Feb 28 12:32:54 2012 -0500 summary: Close split_blast branch
changeset: 7149:1327f2219423 branch: meme_requirement_on_fimo parent: 6662:8ba74c17e809 user: Daniel Blankenberg <dan@bx.psu.edu> date: Fri Feb 03 11:15:29 2012 -0500 summary: close branch
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, January 29, 2013 9:00 AM To: Waldron, Michael H Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
Hi Michael,
The previous post you mention is outdated. The main Galaxy tool shed from which you are pulling has been tracking Galaxy dist for some time now, so you should only have to update to that.
However, the communication layer between Galaxy and the tool shed is backward compatible to the December 20, 2012 Galaxy release, so whether you have updated from Galaxy central or Galaxy dist, you should not be seeing the behavior you describe.
If you do, in fact, track Galaxy central though, and use the main Galaxy tool shed, you may experience some strange behavior because the the development code may include new features that are not available on the main tool shed since it tracks Galaxy dist.
What is the result of typing the following in your Galaxy installation directory?
hg heads
Thanks,
Greg Von Kuster
On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote:
Users are getting the following error when trying to add a tool from the tool shed repository on our local galaxy instance.
"An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)"
The galaxy server log shows the message included below. The main error is "ValueError: too many values to unpack ". From a similar previous post, the resolution was to use the latest code from Galaxy central. I just ran an "hg pull -u" pointing to galaxy-central (we had been pointing to galaxy-dist), but we still get the same error.
Any ideas?
(server log) [29/Jan/2013:08:19:05 -0400] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=f19bc86bac946438&changeset_revisions=2d6671b10919 HTTP/1.1" 500 - "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438&changeset_revision=2d6671b10919" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2" Error - <type 'exceptions.ValueError'>: too many values to unpack URL: https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=f19bc86bac946438&changeset_revisions=2d6671b10919 File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1201 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack
Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill
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