This is a fresh clone, from galaxy-dist, but I have a pile of patch files to keep my local hacks straight. I forgot about the registry.py file. Removed that, as well as the blast import. It's hard to keep local hacks and regular updates in sync...

Thanks,
David

On 3/6/2013 12:16 PM, Dannon Baker wrote:
Is this a fresh clone from galaxy-dist or have you pulled it from somewhere else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py has been altered to have an extra import, 'gmap', for gmap tools.

-Dannon

On Wed, Mar 6, 2013 at 12:08 PM, David Hoover <hoove...@helix.nih.gov <mailto:hoove...@helix.nih.gov>> wrote:

    Hi,

    I'm trying to load an instance of Galaxy from scratch, and I'm
    getting this error message after configuration and typing "./run.sh":

    Traceback (most recent call last):
      File "./scripts/paster.py", line 33, in <module>
        serve.run()
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line
    1056, in run
        invoke(command, command_name, options, args[1:])
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line
    1062, in invoke
        exit_code = runner.run(args)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line
    227, in run
        result = self.command()
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/serve.py", line
    650, in command
        app = loadapp( app_spec, name=app_name, relative_to=base,
    global_conf=vars)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 350, in loadapp
        return loadobj(APP, uri, name=name, **kw)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 374, in loadobj
        global_conf=global_conf)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 399, in loadcontext
        global_conf=global_conf)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 423, in _loadconfig
        return loader.get_context(object_type, name, global_conf)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 561, in get_context
        section)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 620, in _context_from_explicit
        value = import_string(found_expr)
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/util/pastescript/loadwsgi.py",
    line 125, in import_string
        return pkg_resources.EntryPoint.parse("x=" + s).load(False)
      File "/spin1/users/galaxy/galaxy1/lib/pkg_resources.py", line
    1954, in load
        entry = __import__(self.module_name, globals(),globals(),
    ['__name__'])
      File "/spin1/users/galaxy/galaxy1/lib/galaxy/web/buildapp.py",
    line 3, in <module>
        from galaxy.webapps.galaxy.buildapp import app_factory
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/webapps/galaxy/buildapp.py",
    line 18, in <module>
        from galaxy import config, jobs, util, tools
      File "/spin1/users/galaxy/galaxy1/lib/galaxy/jobs/__init__.py",
    line 15, in <module>
        from galaxy import util, model
      File "/spin1/users/galaxy/galaxy1/lib/galaxy/model/__init__.py",
    line 13, in <module>
        import galaxy.datatypes.registry
      File
    "/spin1/users/galaxy/galaxy1/lib/galaxy/datatypes/registry.py",
    line 9, in <module>
        import gmap # added for gmap tools
    ImportError: No module named gmap

    What is missing?

    David Hoover
    Helix Systems Staff
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