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.ba...@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 <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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>
>
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