I am using the default ubuntu 12.04 python.

Andrew Krohn

PhD Candidate, NAU Biological Sciences

Research Technician, EnGGen

On Thu, Jun 6, 2013 at 1:17 PM, Dannon Baker <dannon.baker@gmail.com> wrote:

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

___________________________________________________________
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:
  http://lists.bx.psu.edu/

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