[galaxy-dev] tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

Matthias Bernt Wed, 08 Mar 2017 07:59:19 -0800

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,
m.be...@ufz.de, 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
-------------------------------------------

smime.p7s
Description: S/MIME Cryptographic Signature

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)

Reply via email to