Question: (Closed) galaxy main tool shed "join" installation error
0
gravatar for yu.1.wang
4.2 years ago by
yu.1.wang0
Germany
yu.1.wang0 wrote:

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

 

Will skip URL https://pypi.python.org/simple/numpy/1.7.1 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 https://pypi.python.org/simple/numpy/ 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 https://pypi.python.org/simple/numpy/: 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/__init__.py", 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/basecommand.py", 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/log.py", 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/log.py", 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/__init__.py", line 88, in fwrite
    f.write(s)
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,

Cheers,

Yu

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by yu.1.wang0

There is a Biostar site just for Galaxy. You'll probably have better luck posting this question there.

ADD REPLYlink written 4.2 years ago by Dan D6.7k

Thanks for pointing it out! I reposted it there.

ADD REPLYlink written 4.2 years ago by yu.1.wang0

OP posted question on the Galaxy Biostar after being made aware of it.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Dan D6.7k
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