Hi Lance,

What process did you use for updating the tool shed repository and how many separate repositories did you use?  You should not be updating a local repository, pushing the changes to the tool shed repository, and then attempting to pull the changes back to the same repository.  Your repository environment should be something like this:

DEV REPO ( all development updates are performed here, so this is where the tool version is incremented )
    |
   V
<pushed changeset>
   |
   V
EXISTING TOOL SHED REPO
   |
  V
<pulled changeset to some previously cloned repo>
   |
  V
PREVIOUSLY CLONED (possibly production) REPO

In other words, nothing should ever get pushed and pulled from the tool shed repo into the same repo.  If this is the process you used, it would undoubtedly result in the behavior you saw.  If you used separate repos as I describe above, we'll need more details as to the process you used in order to determine the cause of the problem.

Greg Von Kuster


On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:

I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3.  This version has some functional changes and thus the tool version was incremented.  I installed this new version of the tool in my local Galaxy instance.

However, I realized later that I missed updating one part of the help text. Today I fixed that text (but left the tool version the same), tarred up the file, and uploaded it to the toolshed.  I then attempted to "Get Updates" from my local Galaxy instances for that tool got the following error:

URL: http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=5d969cb56112&latest_changeset_revision=f320093f1e8e&latest_ctx_rev=11
File '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__
environ, self.app)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__
return self.app( environ, start_response )
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 206 in decorator
return func( self, trans, *args, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1677 in update_to_changeset_revision
update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', line 1428 in update_repository
rev=ctx_rev )
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', line 5661 in update
rev = scmutil.revsingle(repo, rev, rev).rev()
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 515 in revsingle
l = revrange(repo, [revspec])
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 588 in revrange
for r in m(repo, range(len(repo))):
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 1414 in mfunc
return getset(repo, subset, tree)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 156 in getset
return methods[x[0]](repo, subset, *x[1:])
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 171 in symbolset
return stringset(repo, subset, x)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 161 in stringset
x = repo[x].rev()
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py', line 235 in __getitem__
return context.changectx(self, changeid)
File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py', line 103 in __init__
_("unknown revision '%s'") % changeid)
RepoLookupError: unknown revision '11'


I believe this is because the revision I have installed (10) is not longer considered a valid revision by the toolshed (I presume since it is an older revision of with the same tool version).

Any help would be appreciated.  Thanks.

-- 
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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