For whatever reason, it looks like your python was compiled without bz2 support. The following links may help you get a usable python installed:
http://stackoverflow.com/questions/12806122/missing-python-bz2-module http://stackoverflow.com/questions/8115280/importerror-no-module-named-bz2-for-python-2-7-2 On Thu, Jun 6, 2013 at 4:19 PM, Andrew Krohn <alk...@nau.edu> wrote: > 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 >>> >>> ___________________________________________________________ >>> 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/ >>> >> >> >
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