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 <alk...@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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