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) ---
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-e...
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-ssle... due to some failed SSL certificate check?
Some help (or ideas for targeted checking) would be great :).
Cheers, Sebastian
On Thu, Feb 11, 2016 at 12:43 PM, Sebastian Schaaf < schaaf@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/requ...
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/requ... ")
--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-e...
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-ssle... 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. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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-excepti.... 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/requ...")
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 < schaaf@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/requ...
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/requ... ")
--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-e...
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-ssle... 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. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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-excepti.... 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/requ...")
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 < schaaf@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/requ...
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/requ... ")
--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-e...
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-ssle... 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. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
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Björn Grüning -
Nate Coraor -
Sebastian Schaaf