Question: galaxy main tool shed "join" installation error
gravatar for
2.4 years ago by
yu.1.wang10 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,



ADD COMMENTlink modified 2.3 years ago by jmchilton1000 • written 2.4 years ago by yu.1.wang10
gravatar for Martin Čech
2.3 years ago by
Martin Čech ♦♦ 3.9k
United States
Martin Čech ♦♦ 3.9k 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 2.3 years ago by Martin Čech ♦♦ 3.9k
gravatar for jmchilton
2.3 years ago by
United States
jmchilton1000 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 2.3 years ago by jmchilton1000
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