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
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