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