How did you install your python, or are you using the default ubuntu 12.04 version?  The bz2 module should be distributed with any python since 2.3.

-Dannon

On Thu, Jun 6, 2013 at 3:25 PM, Andrew Krohn <alk224@nau.edu> wrote:

I looked through others' problems, but this seems unique.  I just did a clean install of Ubuntu 12.04 and wanted to add Galaxy to integrate our various pipelines (16S rRNA via qiime, RADseq data, small genome assemblies).  However, I seem to be stuck at the beginning of the install.  Followed instructions from this page explicitly (http://wiki.galaxyproject.org/Admin/Get%20Galaxy).  When I run sh run.sh, I get the below output, and the server cannot be accessed via web browser.  I am using python 2.7.3.  I opened a python instance and ran import bz2, but then I get the same error (ImportError: No module named bz2).

enggen@OptimusPrime:~/galaxy-dist$ sh run.sh 

Traceback (most recent call last):

  File "./scripts/paster.py", line 33, in <module>

    serve.run()

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run

    invoke(command, command_name, options, args[1:])

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke

    exit_code = runner.run(args)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run

    result = self.command()

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command

    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp

    return loadobj(APP, uri, name=name, **kw)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj

    global_conf=global_conf)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext

    global_conf=global_conf)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig

    return loader.get_context(object_type, name, global_conf)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context

    section)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit

    value = import_string(found_expr)

  File "/home/enggen/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string

    return pkg_resources.EntryPoint.parse("x=" + s).load(False)

  File "/home/enggen/galaxy-dist/lib/pkg_resources.py", line 1954, in load

    entry = __import__(self.module_name, globals(),globals(), ['__name__'])

  File "/home/enggen/galaxy-dist/lib/galaxy/web/buildapp.py", line 3, in <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/enggen/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 17, in <module>

    import galaxy.model

  File "/home/enggen/galaxy-dist/lib/galaxy/model/__init__.py", line 23, in <module>

    import galaxy.datatypes.registry

  File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in <module>

    import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex

  File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 14, in <module>

    from galaxy.datatypes.checkers import is_gzip

  File "/home/enggen/galaxy-dist/lib/galaxy/datatypes/checkers.py", line 1, in <module>

    import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr

ImportError: No module named bz2

Andrew Krohn

PhD Candidate, NAU Biological Sciences

Research Technician, EnGGen

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