Hello Greg

Thanks for the information, great to hear this is already fixed - it's totally fine for us to wait for the next release of Galaxy dist.

More generally I just wanted to say I've used the automated toolshed install for other tools without a problem and think this is a brilliant feature - I really appreciate the huge effort that you guys put into Galaxy.

Thanks & best wishes

Peter

On 23/04/12 15:24, Greg Von Kuster wrote:
Hello Peter,

This issue was fixed a while ago, but has not yet made it to the Galaxy dist 
repository.  Since the dist repository is generally 4 to 6 weeks behind the 
Galaxy central repository, your local Galaxy instance will have to track the 
central repository instead of the dist repository in order to use any features 
that interact between Galaxy and the tool shed.  I believe a new release to the 
dist repository is scheduled for some time in the next week or so, so you can 
wait for it if you want.

Sorry for the inconvenience!

Greg Von Kuster

On Apr 23, 2012, at 5:53 AM, Peter Briggs wrote:

Hello

I've encountered some problems installing and then trying to remove a tool from 
the main toolshed in a local Galaxy production instance. The tool is the 
tmap_wrapper but I don't think that the tool itself is the problem.

When I tried the automated install from the toolshed, the Galaxy window came back with 
"Server error" and in paster.log I found this:

== paster.log fragment start ==
galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,151 Installing repository 
'tmap_wrapper'
galaxy.util.shed_util DEBUG 2012-04-20 15:46:15,186 Cloning 
http://toolshed.g2.bx.psu.edu/repos/nils
homer/tmap_wrapper
galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,114 Updating cloned repository to 
revision "40ade4f81a30"
galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,278 Data 
table named 'tmap_indexes' is required by tool but not configured
galaxy.util.shed_util DEBUG 2012-04-20 15:46:17,322 Adding new row (or updating 
an existing row) for repository 'tmap_wrapper' in the tool_shed_repository 
table.
galaxy.tools.parameters.dynamic_options WARNING 2012-04-20 15:46:17,400 Data 
table named 'tmap_indexes' is required by tool but not configured
130.88.213.137 - - [20/Apr/2012:15:46:15 +0100] "POST 
/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True
 HTTP/1.1" 500 - 
"http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071:7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True";
 "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.1) Gecko/2!
0100101 Fi
refox/10.0.1"
Error -<type 'exceptions.NameError'>: global name 
'handle_sample_tool_data_table_conf_file' is not defined
URL: 
http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=17a5b933699a3c40818076daffd7d763e25e8071%3A7b22746d61705f77726170706572223a205b226d617070696e6720666f7220496f6e20546f7272656e74222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6e696c73686f6d65722f746d61705f77726170706572222c2022343061646534663831613330225d7d&includes_tools=True
File 
'/home/galaxy/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 '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
line 80 in __call__
  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 
line 632 in __call__
  return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in 
__call__
  body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 
in decorator
  return func( self, trans, *args, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', 
line 316 in install_repository
  shed_tool_conf=shed_tool_conf )
File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 890 in 
load_repository_contents
  repository_tools_tups = handle_missing_data_table_entry( trans.app, 
tool_path, sample_files, repository_tools_tups )
File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 753 in 
handle_missing_data_table_entry
  error, correction_msg = handle_sample_tool_data_table_conf_file( app, 
sample_file )
NameError: global name 'handle_sample_tool_data_table_conf_file' is not defined
== paster.log fragment end ==

(I've replaced the machine name in the URLs with X's so our sysadmin won't maim 
me.) It seems that the error is something to do with Galaxy failing to handle 
the tool's tool_data_table_conf.xml.sample.

As far as I can tell the hg clone of the tool worked okay as the files for the 
tool can be found in 
/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nilshomer/tmap_wrapper/40ade4f81a30/tmap_wrapper/tmap_wrapper_0.0.19
 but the tool doesn't appear in the tool panel and isn't referenced in either 
the shed_tool_conf.xml or tool_conf.xml files.

However: the tool does appear under the Admin ->  Manage installed tool shed repositories 
option in Galaxy. Unfortunately attempting to uninstall it via this interface also fails 
with the "Server error" in the Galaxy window. This section of paster.log looks 
relevant here:

== paster.log fragment start ==
Error -<type 'exceptions.TypeError'>: coercing to Unicode: need string or 
buffer, NoneType found
URL: 
http://XXXXXX.XX.XXXXXXXXXX.XX.XX/galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=f2db41e1fa331b3e
File 
'/home/galaxy/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 '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
line 80 in __call__
  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 
line 632 in __call__
  return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in 
__call__
  body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 
in decorator
  return func( self, trans, *args, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', 
line 181 in deactivate_or_uninstall_repository
  remove_from_tool_panel( trans, repository, shed_tool_conf, 
uninstall=remove_from_disk_checked )
File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 989 in 
remove_from_tool_panel
  tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( 
trans, repository )
File '/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py', line 490 in 
generate_tool_panel_dict_from_shed_tool_conf_entries
  tree = util.parse_xml( shed_tool_conf )
File '/home/galaxy/galaxy-dist/lib/galaxy/util/__init__.py', line 105 in 
parse_xml
  tree = ElementTree.parse(fname)
File 
'/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py',
 line 859 in parse
File 
'/home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py',
 line 576 in parse
TypeError: coercing to Unicode: need string or buffer, NoneType found
== paster.log fragment end ==

After this the tool files are still there under the "shed_tools" directory, and the tool 
still appears under "Manage installed tool shed repositories".

We're using the most recent galaxy-dist (hg reports our most recent changeset 
as 6799:40f1816d6857).

I don't know if anyone else has encountered this problem but it would be useful 
to know how to either complete the automated install or else be able to remove 
the tool completely and add it manually for now.

Apologies btw for the long message, thanks for your help - Galaxy is fantastic 
and all the work that has gone into it is very much appreciated!

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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