Question: ValueError I/O in various tool dependencies
0
gravatar for stephane.roche
2.6 years ago by
France
stephane.roche10 wrote:

Hello,

I am facing to an error during the installation of different tool shed package. My distribution of Galaxy is installed on a Xubuntu system. I can not install bx-python 0.7.1, galaxy_sequence_utils, package_galaxy_ops_1_0_0 for nearly the same problem. I can not identified which problem might have my configuration. could you help me ?

Stephane

 

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip", line 8, in <module>
    load_entry_point('pip==1.3.1', 'console_scripts', 'pip')()
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/__init__.py", line 149, in main
    return command.main(args[1:], options)
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/basecommand.py", line 181, in main
    logger.fatal('Storing complete log in %s' % log_fn)
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/log.py", line 48, in fatal
    self.log(self.FATAL, msg, *args, **kw)
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/log.py", line 75, in log
    backwardcompat.fwrite(consumer, rendered)
  File "/home/galaxy/galaxy-dist/tooldependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/backwardcompat/__init__.py", line 88, in fwrite
    f.write(s)
ValueError: I/O operation on closed file

 

software error • 1.0k views
ADD COMMENTlink modified 22 months ago by elritch0 • written 2.6 years ago by stephane.roche10
1
gravatar for jmchilton
2.6 years ago by
jmchilton990
United States
jmchilton990 wrote:

Hmm... I had not seen this before but it looks like (https://github.com/pypa/pip/issues/219) can be caused by running pip without having a writable home directory. Is your Galaxy home directory (looks like /home/galaxy based on stack trace) writable by the user Galaxy is running as (most likely galaxy)?

ADD COMMENTlink written 2.6 years ago by jmchilton990
1
gravatar for stephane.roche
2.5 years ago by
France
stephane.roche10 wrote:

I have found the solution of my problem at 2 levels: in xubuntu, zlib library is not installed and some tools failed to compile and makefile. And last, some eggs in galaxy were not correctly installed. 

I have check both and solve my problem.

Stephane

 

ADD COMMENTlink written 2.5 years ago by stephane.roche10
0
gravatar for irit.le.re
2.1 years ago by
irit.le.re0
European Union
irit.le.re0 wrote:

We have encountered the same problem while installing the same package bx-python 0.7.1.
We have installed the zlib library, but it still give us this error.
Could you elaborate which eggs in galaxy were not correctly installed?

Thanks

Irit

 

ADD COMMENTlink written 2.1 years ago by irit.le.re0
0
gravatar for elritch
22 months ago by
elritch0
Canada
elritch0 wrote:

I am having a very similar problem when trying to use the setup_virtualenv in any dependencies file to use pip for install. I get the exact same error. On my instance, zlib is installed. I have checked out issue 219 as suggested. I know this is a little late but can anyone elaborate on how to resolve this issue.

Thanks,

Elie

ADD COMMENTlink written 22 months ago by elritch0
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