Question: galaxy main tool shed "join" installation error
gravatar for
4.0 years ago by
yu.1.wang20 wrote:

Hi, I am trying to install "join" de21bdbb8d28, from Galaxy main tool shed, but it failed with the following error:

Will skip URL when looking for download links for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
  Will skip URL when looking for download links for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
  Could not find any downloads that satisfy the requirement numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
No distributions at all found for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
Storing complete log in /home/wang/.pip/pip.log
  Could not fetch URL There was a problem confirming the ssl certificate: <urlopen error="" [Errno="" 1]="" _ssl.c:497:="" error:14090086:SSL="" routines:SSL3_GET_SERVER_CERTIFICATE:certificate="" verify="" failed="">
Traceback (most recent call last):
  File "/home/wang/galaxy-dist/tool_deps/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/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/", line 149, in main
    return command.main(args[1:], options)
  File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/", line 181, in main
    logger.fatal('Storing complete log in %s' % log_fn)
  File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/", line 48, in fatal
    self.log(self.FATAL, msg, *args, **kw)
  File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/", line 75, in log
    backwardcompat.fwrite(consumer, rendered)
  File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/backwardcompat/", line 88, in fwrite
ValueError: I/O operation on closed file
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler ERROR 2014-12-17 14:38:54,807 Failed to do setup_virtualenv install, exit code='1'

I am working on SLES 11 SP3. Does anyone know how to fix this? On my OS X, there is no problem to install "join" into galaxy. Thanks,



installation tool shed pacakge • 1.4k views
ADD COMMENTlink modified 3.9 years ago by jmchilton1.1k • written 4.0 years ago by yu.1.wang20
gravatar for Martin Čech
3.9 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

This has probably nothing to do with Galaxy but more with your cert configuration.

Please have a look at and to get some ideas on how to approach it.

ADD COMMENTlink written 3.9 years ago by Martin Čech ♦♦ 4.9k
gravatar for jmchilton
3.9 years ago by
United States
jmchilton1.1k wrote:

Sorry for the late response - I missed this question. So this would seem to be an operating system problem - there is probably something misconfigured with your default operating system certificates - I think there are usually operating system packages that install and configure these properly. Do the following commands work if you execute them on the command-line? If not, is there a system administrator you can ask about whether these certificates have been modified or are up-to-date?

virutalenv testvenv
. testenv/bin/activate
pip install numpy


ADD COMMENTlink written 3.9 years ago by jmchilton1.1k
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