Galaxy installation on ubunto failed while running run.sh

Question: Galaxy installation on ubunto failed while running run.sh

2.9 years ago by

bhargav.cse2012 • 0

bhargav.cse2012 • 0 wrote:

Installing Galaxy on ubuntu 15.0.4 OS. run.sh failed

Activating virtualenv at .venv
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
serve.run()
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in run
invoke(command, command_name, options, args[1:])
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke
exit_code = runner.run(args)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/serve.py", line 223, in run
result = self.command()
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/serve.py", line 639, in command
app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in loadapp
return loadobj(APP, uri, name=name, **kw)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 316, in loadobj
global_conf=global_conf)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 341, in loadcontext
global_conf=global_conf)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 365, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 503, in get_context
section)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 562, in _context_from_explicit
value = import_string(found_expr)
File "/home/galaxy/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 122, in import_string
return pkg_resources.EntryPoint.parse("x=" + s).load(False)
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2312, in load
return self.resolve()
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2318, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/home/galaxy/galaxy/lib/galaxy/web/buildapp.py", line 5, in <module>
from galaxy.webapps.galaxy.buildapp import app_factory
File "/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>
import galaxy.app
File "/home/galaxy/galaxy/lib/galaxy/app.py", line 14, in <module>
from galaxy.visualization.data_providers.registry import DataProviderRegistry
File "/home/galaxy/galaxy/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module>
from galaxy.visualization.data_providers import genome
File "/home/galaxy/galaxy/lib/galaxy/visualization/data_providers/genome.py", line 15, in <module>
from bx.bbi.bigbed_file import BigBedFile
ImportError: No module named bigbed_file

4:45:03 PM

Regards

Bhargav

software error galaxy • 1.3k views

ADD COMMENT • link •

modified 2.4 years ago by irmny • 0 • written 2.9 years ago by bhargav.cse2012 • 0

Following-up on this issue. Ubuntu 14.04.5 and latest clone of Galaxy. Confirmed proper installation of numpy-1.11.3 and bx-python-0.7.3 but still get the following error up start up with sudo sh run.sh --no-replace-pip:

ImportError: No module named bigbed_file

How does this get resolved, galaxy experts?

ADD REPLY • link written 23 months ago by njoebott • 30

2.8 years ago by

e.rempel • 30

Germany

e.rempel • 30 wrote:

I had a similar error message running a python script. I fixed it by installing python module "bx-python" via "pip" as follows

pip install bx-python

Be sure that you have the package "numpy" previously installed.

Regards,

Eugen Rempel

ADD COMMENT • link written 2.8 years ago by e.rempel • 30

2.4 years ago by

zipho • 0

zipho • 0 wrote:

This is still an issue for me.

I have a fresh galaxy clone on an ubuntu system.

When attempting:

pip install bx-python

Seem like I have bx-python already.

Requirement already satisfied (use --upgrade to upgrade): bx-python in

Regards Z

ADD COMMENT • link written 2.4 years ago by zipho • 0

2.4 years ago by

irmny • 0

irmny • 0 wrote:

Had the same problem which was solved by:

pip uninstall bx-python

pip install bx-python

The problem is potentially in the requirements.txt file which seems to "require" bx-python before numpy. As Eugen mentioned in the previous answer numpy needs to be installed before bx-python. Hope this helps.

Cheers, Ian

ADD COMMENT • link written 2.4 years ago by irmny • 0

I have the same issue now on a CentOS 7 instance:

File "/home/galaxy/galaxy/lib/galaxy/visualization/data_providers/genome.py", line 15, in <module> from bx.bbi.bigbed_file import BigBedFile ImportError: No module named bigbed_file

I've done the uninstall and reinstall of numpy and bx-python in the both the /usr environment (/usr/bin/pip) and the virtualenv (/home/galaxy/galaxy/.venv/bin/pip) to no avail.

ADD REPLY • link written 2.4 years ago by njoebott • 30

specifically what I did was:

/dir/stuff/galaxy/.venv/bin/pip uninstall bx-python

/dir/stuff/galaxy/.venv/bin/pip install --upgrade ~/Downloads/numpy-1.9.2.tar.gz

/dir/stuff/galaxy/.venv/bin/pip install --upgrade ~/Downloads/bx-python-0.7.3.tar.gz

Note that I am behind a pretty heavy firewall so have to install from tarballs downloaded from https://wheels.galaxyproject.org/simple. Also, I too am on Centos 7. Good luck

ADD REPLY • link modified 2.4 years ago • written 2.4 years ago by irmny • 0

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