On Thu, Feb 11, 2016 at 12:43 PM, Sebastian Schaaf <
sch...@ibe.med.uni-muenchen.de> wrote:

> Hey all,
>
> I am currently trying to install Gemini (v0.18.1) via the test toolshed.
> It finally fails in dependencies as 'package_gemini_0_18_1' finds
> dependency 'gemini' to end in error state. There the message looks like
> the following:
>
> ---
> 2016-02-11 16:34:47 (72.4 MB/s) - `Miniconda-latest-Linux-x86_64.sh' saved
> [25416725/25416725]
>
> Python 2.7.11 :: Continuum Analytics, Inc.
> Traceback (most recent call last):
>   File "gemini_install.py", line 190, in <module>
>     main(parser.parse_args())
>   File "gemini_install.py", line 80, in main
>     gemini = install_conda_pkgs(anaconda, remotes, args)
>   File "gemini_install.py", line 97, in install_conda_pkgs
>     urllib.urlretrieve(remotes["requirements_conda"], filename=req_file)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
> 98, in urlretrieve
>     return opener.retrieve(url, filename, reporthook, data)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
> 245, in retrieve
>     fp = self.open(url, data)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
> 213, in open
>     return getattr(self, name)(url)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line
> 443, in open_https
>     h.endheaders(data)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
> 1049, in endheaders
>     self._send_output(message_body)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
> 893, in _send_output
>     self.send(msg)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
> 855, in send
>     self.connect()
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
> 1274, in connect
>     server_hostname=server_hostname)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 352,
> in wrap_socket
>     _context=self)
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 579,
> in __init__
>     self.do_handshake()
>   File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 808,
> in do_handshake
>     self._sslobj.do_handshake()
> IOError: [Errno socket error] [SSL: UNKNOWN_PROTOCOL] unknown protocol
> (_ssl.c:590)
> ---
>

Hi Sebastian,

I believe the URL that it's attempting to fetch is:


https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requirements_conda.txt

Using the Python interpreter that your Galaxy instance is using, what
happens if you do:

  >>> import urllib
  >>> urllib.urlretrieve("
https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requirements_conda.txt
")

--nate


>
> Some browsing at Google brought hints on three common cases where this
> could appear *plus* a fourth one which looks by error code pretty much
> what I got:
>
>
> http://blog.techstacks.com/2010/03/3-common-causes-of-unknown-ssl-protocol-errors-with-curl.html
>
> So, may I be right that there is a typo in an URL needed for downloading
> during the setup process? Or is it, according to
>
> http://stackoverflow.com/questions/10667960/python-requests-throwing-up-sslerror
> due to some failed SSL certificate check?
>
> Some help (or ideas for targeted checking) would be great :).
>
> Cheers,
> Sebastian
>
> --
> Sebastian Schaaf, M.Sc. Bioinformatics
> Faculty Coordinator NGS Infrastructure
> Chair of Biometry and Bioinformatics
> Department of Medical Informatics,
>  Biometry and Epidemiology (IBE)
> University of Munich
> DKTK Munich
> Marchioninistr. 15, K U1 808
> D-81377 Munich (Germany)
> Tel: +49 89 4400 77499
>
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