local install problem
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
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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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/
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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-f... On Thu, Jun 6, 2013 at 4:19 PM, Andrew Krohn <alk224@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.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/
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participants (2)
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Andrew Krohn -
Dannon Baker