galaxyproject / galaxyproject/galaxy

500 errors when updating tools via "manage installed tools", "get updates"

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Description

e.g. macs2

```
galaxy.tools.deps.conda_util DEBUG 2017-05-31 18:09:54,983 Executing command: /mnt/galaxy/data/galaxy/tool-deps/_conda/bin/conda create -y --name __macs2@2.1.1.20160309 macs2=2.1.1.20160309
172.17.131.103 - - [31/May/2017:18:09:52 -0400] "GET /admin_toolshed/update_to_changeset_revision?name=subtract&latest_ctx_rev=4&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=c19a2a29c561&latest_changeset_revision=7a2a604ae9c8 HTTP/1.0" 500 - "http://galaxy.neb.com/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:53.0) Gecko/20100101 Firefox/53.0"
Error - : 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)
URL: http://galaxy.neb.com/admin_toolshed/update_to_changeset_revision?name=subtract&latest_ctx_rev=4&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=c19a2a29c561&latest_changeset_revision=7a2a604ae9c8
File '/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__
app_iter = self.application(environ, sr_checker)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 191 in __call__
return self.app( environ, start_response )
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 135 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 214 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy/lib/galaxy/web/framework/decorators.py', line 98 in decorator
return func( self, trans, *args, **kwargs )
File '/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1897 in update_to_changeset_revision
hg_util.update_repository( repo, latest_ctx_rev )
File '/home/galaxy/galaxy/lib/tool_shed/util/hg_util.py', line 462 in update_repository
commands.update( get_configured_ui(), repo, rev=ctx_rev )
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py', line 6973 in update
ret = hg.update(repo, rev)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py', line 680 in update
stats = updaterepo(repo, node, False)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py', line 676 in updaterepo
labels=['working copy', 'destination'])
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 1532 in update
stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 1196 in applyupdates
complete, r = ms.preresolve(f, wctx, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 502 in preresolve
return self._resolve(True, dfile, wctx, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 457 in _resolve
labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 680 in premerge
return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 627 in _filemerge
r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 324 in _premerge
r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py', line 397 in simplemerge
out = opener(os.path.basename(local), "w", atomictemp=True)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py', line 530 in __call__
self.audit(path)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py', line 61 in __call__
or _lowerclean(parts[0]) in ('.hg', '.hg.', '')
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py', line 16 in _lowerclean
return encoding.hfsignoreclean(s.lower())
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py', line 35 in hfsignoreclean
if "\xe2" in s or "\xef" in s:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)
```

picard
```
172.17.131.103 - - [31/May/2017:18:12:18 -0400] "GET /admin_toolshed/update_to_changeset_revision?name=picard&latest_ctx_rev=4&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=e0232cbac965&latest_changeset_revision=ab1f60c26526 HTTP/1.0" 500 - "http://galaxy.neb.com/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:53.0) Gecko/20100101 Firefox/53.0"
Error - : 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)
URL: http://galaxy.neb.com/admin_toolshed/update_to_changeset_revision?name=picard&latest_ctx_rev=4&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=e0232cbac965&latest_changeset_revision=ab1f60c26526
File '/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__
app_iter = self.application(environ, sr_checker)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 191 in __call__
return self.app( environ, start_response )
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 135 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy/lib/galaxy/web/framework/base.py', line 214 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/galaxy/lib/galaxy/web/framework/decorators.py', line 98 in decorator
return func( self, trans, *args, **kwargs )
File '/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1897 in update_to_changeset_revision
hg_util.update_repository( repo, latest_ctx_rev )
File '/home/galaxy/galaxy/lib/tool_shed/util/hg_util.py', line 462 in update_repository
commands.update( get_configured_ui(), repo, rev=ctx_rev )
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py', line 6973 in update
ret = hg.update(repo, rev)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py', line 680 in update
stats = updaterepo(repo, node, False)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py', line 676 in updaterepo
labels=['working copy', 'destination'])
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 1532 in update
stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 1196 in applyupdates
complete, r = ms.preresolve(f, wctx, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 502 in preresolve
return self._resolve(True, dfile, wctx, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py', line 457 in _resolve
labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 680 in premerge
return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 627 in _filemerge
r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py', line 324 in _premerge
r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py', line 397 in simplemerge
out = opener(os.path.basename(local), "w", atomictemp=True)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py', line 530 in __call__
self.audit(path)
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py', line 61 in __call__
or _lowerclean(parts[0]) in ('.hg', '.hg.', '')
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py', line 16 in _lowerclean
return encoding.hfsignoreclean(s.lower())
File '/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py', line 35 in hfsignoreclean
if "\xe2" in s or "\xef" in s:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128)
```

some do work...

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