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

Already in the email thread. Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill ________________________________________ From: james(a)taylorlab.org [james(a)taylorlab.org] on behalf of James Taylor [james(a)jamestaylor.org] Sent: Tuesday, January 29, 2013 11:04 AM To: Waldron, Michael H Cc: Greg Von Kuster; galaxy-dev(a)bx.psu.edu Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository Can you send the output of hg heads after having run the pull -u ? Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H <mwaldron(a)email.unc.edu&gt; 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. > > > 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/