Dear mailing list,

I'm experimenting with the tools available at the Tool Shed and ran into problems with two of the tools.

1. data_manager_fetch_ncbi_taxonomy

If I run the data manager I get an error in the browser: "Uncaught exception in exposed API method"

The terminal shows the following stack trace:

Traceback (most recent call last):
File "/home/berntm/galaxy/lib/galaxy/web/framework/", line 282, in decorator
    rval = func( self, trans, *args, **kwargs )
File "/home/berntm/galaxy/lib/galaxy/webapps/galaxy/api/", line 98, in build
    return tool.to_json(trans, kwd.get('inputs', kwd))
File "/home/berntm/galaxy/lib/galaxy/tools/", line 1853, in to_json
    tools = )
File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/", line 492, in get_loaded_tools_by_lineage
    tool_lineage = self._lineage_map.get( tool_id )
File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/", line 38, in get
    lineage = ToolShedLineage.from_tool_id(, tool_id )
File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/", line 70, in from_tool_id
    return ToolShedLineage( app, tool_version )
File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/", line 53, in __init__
    self.tool_version_id =
File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/", line 237, in __get__
    return self.impl.get(instance_state(instance), dict_)
File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/", line 578, in get
    value = state._load_expired(state, passive)
File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/", line 474, in _load_expired
    self.manager.deferred_scalar_loader(self, toload)
File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/", line 610, in load_scalar_attributes
DetachedInstanceError: Instance <ToolVersion at 0x7fc7180b5310> is not bound to a Session; attribute refresh operation cannot proceed

Any ideas whats going on - and how to fix this?

2. The second tool is ggplot2_2_2_1. Here mingchen0919 is listed as owner in the Tool Shed -- so I do not know if this mailing list is the correct address. If not: how do I find contact information to the owner of a tool in the ToolShed?

Otherwise, the problem is missing dependencies:

In package_fontconfig_2_11_1 (which is a dependency of ggplot) I get

configure: error: in `/home/berntm/galaxy/database/tmp/tmp-toolshed-mtdBsL0ig/fontconfig-2.11.1': configure: error: The pkg-config script could not be found or is too old. Make sure it
is in your PATH or set the PKG_CONFIG environment variable to the full
path to pkg-config.

Alternatively, you may set the environment variables FREETYPE_CFLAGS
and FREETYPE_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

To get pkg-config, see <>.
See `config.log' for more details

Is pkg-config supposed to be installed on the computer running galaxy? Or should this be installed within galaxy?

In addition on the terminal the following error appears after the pkg-config error:

Exception happened during processing of request from ('', 42534)
Traceback (most recent call last):
File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/paste/", line 1085, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/", line 331, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/", line 654, in __init__
  File "/usr/lib/python2.7/", line 713, in finish
  File "/usr/lib/python2.7/", line 283, in close
  File "/usr/lib/python2.7/", line 307, in flush
error: [Errno 32] Broken pipe

Thank you very much for your help.

Best regards,


Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,,

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann

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