Hi Sebastian, can you check your python version and update it if possible. It seems to be an anaconda problem as far as I can see and not related to Galaxy as we do not install this python version... Also try to use the system-python version.
Hope this helps, Bjoern Am 13.02.2016 um 17:10 schrieb Sebastian Schaaf: > Hi Nate, > > Great to read from you :). > > In the time between my request and your answer I tried out some things > starting from the codes and googled a lot. As I left the desk soon after I > could add it up to now. I'll try to keep it short and as comprehensible as > possible: > > * The issue is related to Python itself, not necessarely Unix. 'wget' on > the URL you also used works fine, so proxying is ok. > * There are bugreports on the 'urllib' libraries (there are three of > them), for the two older ones there is no indication for a fix. Here > https://github.com/kennethreitz/requests/issues/1204 > a bug report on the 'requests' module appears, the guys where waiting for > a fix in 'urllib3' (which was finally introduced). But: the tool shed > package comes around with libraries 'urllib' ad 'urllib2', only. > * Generally, it looks like the issue is due to a default behaviour of > Python 2.x's 'ssl' module that may have been no problem in the past: the > handshake is by default performed with SSLv2.3. As on a rising number of > servers SSLv2 gets deactivated for security reasons, connections fail > (SSLv3 is expected and maybe sent - client and server don't unterstand > each other anymore). Check out the second and third highest ranked answer > on this issue: > http://stackoverflow.com/questions/14102416/python-requests-requests-exceptions-sslerror-errno-8-ssl-c504-eof-occurred. > The second also includes a link to relevant line of code. For me it sounds > reasonable, but I am a relative noob on web protocols... > > Consequently, the answer to your question is the following: > > --- >>>> import urllib >>>> urllib.urlretrieve("https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requirements_conda.txt";) > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/usr/lib64/python2.6/urllib.py", line 93, in urlretrieve > return _urlopener.retrieve(url, filename, reporthook, data) > File "/usr/lib64/python2.6/urllib.py", line 239, in retrieve > fp = self.open(url, data) > File "/usr/lib64/python2.6/urllib.py", line 207, in open > return getattr(self, name)(url) > File "/usr/lib64/python2.6/urllib.py", line 441, in open_https > h.endheaders() > File "/usr/lib64/python2.6/httplib.py", line 914, in endheaders > self._send_output() > File "/usr/lib64/python2.6/httplib.py", line 786, in _send_output > self.send(msg) > File "/usr/lib64/python2.6/httplib.py", line 745, in send > self.connect() > File "/usr/lib64/python2.6/httplib.py", line 1122, in connect > self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file) > File "/usr/lib64/python2.6/ssl.py", line 338, in wrap_socket > suppress_ragged_eofs=suppress_ragged_eofs) > File "/usr/lib64/python2.6/ssl.py", line 120, in __init__ > self.do_handshake() > File "/usr/lib64/python2.6/ssl.py", line 279, in do_handshake > self._sslobj.do_handshake() > IOError: [Errno socket error] [Errno 1] _ssl.c:497: error:140770FC:SSL > routines:SSL23_GET_SERVER_HELLO:unknown protocol > --- > > I also encountered the same error message when I try to install or update > Python packages via 'easy_install' or 'pip' - both cannot connect to > repositories. Also I don't know if the failed handshake is at the target > server or our proxy - any idea for a command to check this? > > Finally, I am running out of ideas what to do, for me it looks like it is > too deep in the code for establishing a general workaround. On top, if I > interpreted correctly the findings from the above bullet point list, this > may have an impact on many pieces of software. For every case, where > Python 2.x-driven instances try to access repositories on servers not > offering SSLv2 anymore (maybe via proxy server). > > Ideas? :) > > Cheers, > Sebastian > > >> 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 >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. 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