Re: [galaxy-dev] Error trying to add tools from tool shed respository

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(a)bx.psu.edu] Sent: Tuesday, January 29, 2013 10:07 AM To: Waldron, Michael H Cc: galaxy-dev(a)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(a)bx.psu.edu] > Sent: Tuesday, January 29, 2013 9:52 AM > To: Waldron, Michael H > Cc: galaxy-dev(a)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(a)bx.psu.edu] >> Sent: Tuesday, January 29, 2013 9:12 AM >> To: Waldron, Michael H >> Cc: galaxy-dev(a)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(a)emory.edu&gt; >>> 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(a)me.com&gt; >>> 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(a)me.com&gt; >>> 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(a)me.com&gt; >>> 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(a)me.com&gt; >>> 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(a)bx.psu.edu&gt; >>> 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(a)bx.psu.edu] >>> Sent: Tuesday, January 29, 2013 9:00 AM >>> To: Waldron, Michael H >>> Cc: galaxy-dev(a)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_u... >>>> 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 >>>> >>>> ___________________________________________________________ >>>> 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/ >>> >>> >> >> > > ___________________________________________________________ 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/