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

Python 2.7.11 :: Continuum Analytics, Inc.
Traceback (most recent call last):
  File "gemini_install.py", line 190, in <module>
  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
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
1049, in endheaders
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
893, in _send_output
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
855, in send
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line
1274, in connect
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 352,
in wrap_socket
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 579,
in __init__
  File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 808,
in do_handshake
IOError: [Errno socket error] [SSL: UNKNOWN_PROTOCOL] unknown protocol

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:


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
due to some failed SSL certificate check?

Some help (or ideas for targeted checking) would be great :).


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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