tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

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tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

Matthias Bernt
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/decorators.py",
line 282, in decorator
     rval = func( self, trans, *args, **kwargs )
   File "/home/berntm/galaxy/lib/galaxy/webapps/galaxy/api/tools.py",
line 98, in build
     return tool.to_json(trans, kwd.get('inputs', kwd))
   File "/home/berntm/galaxy/lib/galaxy/tools/__init__.py", line 1853,
in to_json
     tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id )
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", 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/factory.py", line
38, in get
     lineage = ToolShedLineage.from_tool_id( self.app, tool_id )
   File
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py",
line 70, in from_tool_id
     return ToolShedLineage( app, tool_version )
   File
"/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py",
line 53, in __init__
     self.tool_version_id = tool_version.id
   File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py",
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/attributes.py",
line 578, in get
     value = state._load_expired(state, passive)
   File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/state.py",
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/loading.py",
line 610, in load_scalar_attributes
     (state_str(state)))
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 <http://pkg-config.freedesktop.org/>.
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 ('127.0.0.1', 42534)
Traceback (most recent call last):
   File
"/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py",
line 1085, in process_request_in_thread
     self.finish_request(request, client_address)
   File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request
     self.RequestHandlerClass(request, client_address, self)
   File "/usr/lib/python2.7/SocketServer.py", line 654, in __init__
     self.finish()
   File "/usr/lib/python2.7/SocketServer.py", line 713, in finish
     self.wfile.close()
   File "/usr/lib/python2.7/socket.py", line 283, in close
     self.flush()
   File "/usr/lib/python2.7/socket.py", line 307, in flush
     self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
"""

Thank you very much for your help.

Best regards,
Matthias


--

-------------------------------------------
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,
[hidden email], www.ufz.de

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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