Re: [galaxy-dev] Starting uWSGI
If you'd like to send them directly to me off-list I'd be happy to take a look. -Dannon On Tue Feb 17 2015 at 2:50:15 PM Nicholas Kline wrote: > Hi Dannon, > > Thanks for the reply. So I went ahead and verified a few things, as > you requested: > > 1. config files: > > /home/galaxy/galaxy-dist/config/galaxy.ini.sample > /home/galaxy/galaxy-dist/universe_wsgi.ini > > I have only been working with universe_wsgi.ini > > 2. static_enabled > > The content of that line looks exactly as follows: > > static_enabled = False > > 3. I also verified that it exists in the [app:main] section of > universe_wsgi.ini > > I would be willing to post my nginx and universe_wsgi.ini configs, > preferably in private, if that would be helpful with troubleshooting. > Thanks for your help! > > > > > > On Tue, Feb 17, 2015 at 11:27 AM, Dannon Baker > wrote: > > Hi Nicholas, > > > > Odd, I see you're using universe_wsgi.ini. Can you confirm that no > > /config/galaxy.ini file exists? These configurations were > > migrated a little while ago, and if you have multiple configuration files > > that might explain why we're seeing this error. > > > > Other than that, when you set static_enabled = False in your > configuration > > file, you uncommented the existing line, right? That is, this entry in > the > > config file is still in the [app:main] section? > > > > -Dannon > > > > On Mon Feb 16 2015 at 2:10:14 PM Nicholas Kline wrote: > >> > >> Hi Nate, > >> > >> So I went ahead and set `static_enabled = False` in universe_wsgi.ini, > >> restarted uWSGI, and browsed to localhost. I'm including the results > >> of each step below: > >> > >> After restarting uWSGI, the last few lines of uwsgi.log looked like > this: > >> > >> WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter > >> 0xa934c0 pid: 3561 (default app) > >> *** uWSGI is running in multiple interpreter mode *** > >> spawned uWSGI master process (pid: 3561) > >> spawned uWSGI worker 1 (pid: 3575, cores: 4) > >> spawned uWSGI worker 2 (pid: 3576, cores: 4) > >> spawned uWSGI worker 3 (pid: 3583, cores: 4) > >> spawned uWSGI worker 4 (pid: 3587, cores: 4) > >> spawned uWSGI worker 5 (pid: 3591, cores: 4) > >> spawned uWSGI worker 6 (pid: 3595, cores: 4) > >> spawned uWSGI worker 7 (pid: 3599, cores: 4) > >> spawned uWSGI worker 8 (pid: 3603, cores: 4) > >> spawned uWSGI worker 9 (pid: 3607, cores: 4) > >> spawned uWSGI worker 10 (pid: 3611, cores: 4) > >> *** Stats server enabled on 127.0.0.1:9191 fd: 30 *** > >> > >> ...so no traceback this time! > >> > >> Then, browsing to localhost redirects to https://localhost and finally > >> returns: > >> > >> "Internal Server Error Galaxy was unable to successfully complete > >> your request An error occurred. This may be an intermittent problem > >> due to load or other > >> unpredictable factors, reloading the page may address the problem. The > >> error has been logged to our team." > >> > >> That request was logged to uwsgi.log: > >> > >> 127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 - > >> "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101 > >> Firefox/35.0" > >> Error - : 'SCRIPT_NAME' > >> URL: https://localhost/ > >> File 'lib/galaxy/web/framework/middleware/error.py', line 149 in > >> __call__ > >> app_iter = self.application(environ, sr_checker) > >> File > >> '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/ > paste/recursive.py', > >> line 84 in __call__ > >> return self.application(environ, start_response) > >> File > >> '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/ > paste/httpexceptions.py', > >> line 633 in __call__ > >> return self.application(environ, start_response) > >> File 'lib/galaxy/web/framework/base.py', line 132 in __call__ > >> return self.handle_request( environ, start_response ) > >> File 'lib/galaxy/web/framework/base.py', line 159 in handle_request > >> trans = self.transaction_factory( environ ) > >> File 'lib/galaxy/web/framework/webapp.py', line 71 in > >> self.set_transaction_factory( lambda e: > >> self.transaction_chooser( e, galaxy_app, session_cookie ) ) > >> File 'lib/galaxy/web/framework/webapp.py', line 102 in > >> transaction_chooser > >> return GalaxyWebTransaction( environ, galaxy_app, self, > >> session_cookie ) > >> File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__ > >> self._ensure_logged_in_user( environ, session_cookie ) > >> File 'lib/galaxy/web/framework/webapp.py', line 441 in > >> _ensure_logged_in_user > >> if self.request.path.startswith( external_display_path ): > >> File 'lib/galaxy/web/framework/base.py', line 258 in __get__ > >> value = self.func( obj ) > >> File 'lib/galaxy/web/framework/base.py', line 341 in path > >> return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] > >> KeyError: 'SCRIPT_NAME' > >> >
Re: [galaxy-dev] Starting uWSGI
Hi Dannon, Thanks for the reply. So I went ahead and verified a few things, as you requested: 1. config files: /home/galaxy/galaxy-dist/config/galaxy.ini.sample /home/galaxy/galaxy-dist/universe_wsgi.ini I have only been working with universe_wsgi.ini 2. static_enabled The content of that line looks exactly as follows: static_enabled = False 3. I also verified that it exists in the [app:main] section of universe_wsgi.ini I would be willing to post my nginx and universe_wsgi.ini configs, preferably in private, if that would be helpful with troubleshooting. Thanks for your help! On Tue, Feb 17, 2015 at 11:27 AM, Dannon Baker wrote: > Hi Nicholas, > > Odd, I see you're using universe_wsgi.ini. Can you confirm that no > /config/galaxy.ini file exists? These configurations were > migrated a little while ago, and if you have multiple configuration files > that might explain why we're seeing this error. > > Other than that, when you set static_enabled = False in your configuration > file, you uncommented the existing line, right? That is, this entry in the > config file is still in the [app:main] section? > > -Dannon > > On Mon Feb 16 2015 at 2:10:14 PM Nicholas Kline wrote: >> >> Hi Nate, >> >> So I went ahead and set `static_enabled = False` in universe_wsgi.ini, >> restarted uWSGI, and browsed to localhost. I'm including the results >> of each step below: >> >> After restarting uWSGI, the last few lines of uwsgi.log looked like this: >> >> WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter >> 0xa934c0 pid: 3561 (default app) >> *** uWSGI is running in multiple interpreter mode *** >> spawned uWSGI master process (pid: 3561) >> spawned uWSGI worker 1 (pid: 3575, cores: 4) >> spawned uWSGI worker 2 (pid: 3576, cores: 4) >> spawned uWSGI worker 3 (pid: 3583, cores: 4) >> spawned uWSGI worker 4 (pid: 3587, cores: 4) >> spawned uWSGI worker 5 (pid: 3591, cores: 4) >> spawned uWSGI worker 6 (pid: 3595, cores: 4) >> spawned uWSGI worker 7 (pid: 3599, cores: 4) >> spawned uWSGI worker 8 (pid: 3603, cores: 4) >> spawned uWSGI worker 9 (pid: 3607, cores: 4) >> spawned uWSGI worker 10 (pid: 3611, cores: 4) >> *** Stats server enabled on 127.0.0.1:9191 fd: 30 *** >> >> ...so no traceback this time! >> >> Then, browsing to localhost redirects to https://localhost and finally >> returns: >> >> "Internal Server Error Galaxy was unable to successfully complete >> your request An error occurred. This may be an intermittent problem >> due to load or other >> unpredictable factors, reloading the page may address the problem. The >> error has been logged to our team." >> >> That request was logged to uwsgi.log: >> >> 127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 - >> "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101 >> Firefox/35.0" >> Error - : 'SCRIPT_NAME' >> URL: https://localhost/ >> File 'lib/galaxy/web/framework/middleware/error.py', line 149 in >> __call__ >> app_iter = self.application(environ, sr_checker) >> File >> '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> line 84 in __call__ >> return self.application(environ, start_response) >> File >> '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> line 633 in __call__ >> return self.application(environ, start_response) >> File 'lib/galaxy/web/framework/base.py', line 132 in __call__ >> return self.handle_request( environ, start_response ) >> File 'lib/galaxy/web/framework/base.py', line 159 in handle_request >> trans = self.transaction_factory( environ ) >> File 'lib/galaxy/web/framework/webapp.py', line 71 in >> self.set_transaction_factory( lambda e: >> self.transaction_chooser( e, galaxy_app, session_cookie ) ) >> File 'lib/galaxy/web/framework/webapp.py', line 102 in >> transaction_chooser >> return GalaxyWebTransaction( environ, galaxy_app, self, >> session_cookie ) >> File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__ >> self._ensure_logged_in_user( environ, session_cookie ) >> File 'lib/galaxy/web/framework/webapp.py', line 441 in >> _ensure_logged_in_user >> if self.request.path.startswith( external_display_path ): >> File 'lib/galaxy/web/framework/base.py', line 258 in __get__ >> value = self.func( obj ) >> File 'lib/galaxy/web/framework/base.py', line 341 in path >> return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] >> KeyError: 'SCRIPT_NAME' >> >> >> CGI Variables >> - >> DOCUMENT_ROOT: '/usr/share/nginx/html' >> HTTP_ACCEPT: >> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' >> HTTP_ACCEPT_ENCODING: 'gzip, deflate' >> HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' >> HTTP_CONNECTION: 'keep-alive' >> HTTP_HOST: 'localhost' >> HTTP_USER_AGENT: 'Mozilla/5.0
Re: [galaxy-dev] Starting uWSGI
Hi Nicholas, Odd, I see you're using universe_wsgi.ini. Can you confirm that no /config/galaxy.ini file exists? These configurations were migrated a little while ago, and if you have multiple configuration files that might explain why we're seeing this error. Other than that, when you set static_enabled = False in your configuration file, you uncommented the existing line, right? That is, this entry in the config file is still in the [app:main] section? -Dannon On Mon Feb 16 2015 at 2:10:14 PM Nicholas Kline wrote: > Hi Nate, > > So I went ahead and set `static_enabled = False` in universe_wsgi.ini, > restarted uWSGI, and browsed to localhost. I'm including the results > of each step below: > > After restarting uWSGI, the last few lines of uwsgi.log looked like this: > > WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter > 0xa934c0 pid: 3561 (default app) > *** uWSGI is running in multiple interpreter mode *** > spawned uWSGI master process (pid: 3561) > spawned uWSGI worker 1 (pid: 3575, cores: 4) > spawned uWSGI worker 2 (pid: 3576, cores: 4) > spawned uWSGI worker 3 (pid: 3583, cores: 4) > spawned uWSGI worker 4 (pid: 3587, cores: 4) > spawned uWSGI worker 5 (pid: 3591, cores: 4) > spawned uWSGI worker 6 (pid: 3595, cores: 4) > spawned uWSGI worker 7 (pid: 3599, cores: 4) > spawned uWSGI worker 8 (pid: 3603, cores: 4) > spawned uWSGI worker 9 (pid: 3607, cores: 4) > spawned uWSGI worker 10 (pid: 3611, cores: 4) > *** Stats server enabled on 127.0.0.1:9191 fd: 30 *** > > ...so no traceback this time! > > Then, browsing to localhost redirects to https://localhost and finally > returns: > > "Internal Server Error Galaxy was unable to successfully complete > your request An error occurred. This may be an intermittent problem > due to load or other > unpredictable factors, reloading the page may address the problem. The > error has been logged to our team." > > That request was logged to uwsgi.log: > > 127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 - > "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101 > Firefox/35.0" > Error - : 'SCRIPT_NAME' > URL: https://localhost/ > File 'lib/galaxy/web/framework/middleware/error.py', line 149 in > __call__ > app_iter = self.application(environ, sr_checker) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/ > paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/ > paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File 'lib/galaxy/web/framework/base.py', line 132 in __call__ > return self.handle_request( environ, start_response ) > File 'lib/galaxy/web/framework/base.py', line 159 in handle_request > trans = self.transaction_factory( environ ) > File 'lib/galaxy/web/framework/webapp.py', line 71 in > self.set_transaction_factory( lambda e: > self.transaction_chooser( e, galaxy_app, session_cookie ) ) > File 'lib/galaxy/web/framework/webapp.py', line 102 in > transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self, > session_cookie ) > File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__ > self._ensure_logged_in_user( environ, session_cookie ) > File 'lib/galaxy/web/framework/webapp.py', line 441 in > _ensure_logged_in_user > if self.request.path.startswith( external_display_path ): > File 'lib/galaxy/web/framework/base.py', line 258 in __get__ > value = self.func( obj ) > File 'lib/galaxy/web/framework/base.py', line 341 in path > return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] > KeyError: 'SCRIPT_NAME' > > > CGI Variables > - > DOCUMENT_ROOT: '/usr/share/nginx/html' > HTTP_ACCEPT: > 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > HTTP_ACCEPT_ENCODING: 'gzip, deflate' > HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' > HTTP_CONNECTION: 'keep-alive' > HTTP_HOST: 'localhost' > HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; > rv:35.0) Gecko/20100101 Firefox/35.0' > PATH_INFO: '/' > REMOTE_ADDR: '127.0.0.1' > REMOTE_PORT: '50064' > REQUEST_METHOD: 'GET' > REQUEST_URI: '/' > SERVER_NAME: 'localhost' > SERVER_PORT: '443' > SERVER_PROTOCOL: 'HTTP/1.1' > UWSGI_SCHEME: 'https' > > > WSGI Variables > -- > application: 0x7f2ec2f32290> > is_api_request: False > paste.cookies: (, '') > paste.expected_exceptions: [ HTTPException'>] > paste.httpexceptions: object at 0x7f2ec2f32210> > paste.recursive.forward: > paste.recursive.include: > paste.recursive.include_app_iter: from /> > paste.recursive.script_name: '' > paste.
[galaxy-dev] Starting uWSGI
Hi Nate,
So I went ahead and set `static_enabled = False` in universe_wsgi.ini,
restarted uWSGI, and browsed to localhost. I'm including the results
of each step below:
After restarting uWSGI, the last few lines of uwsgi.log looked like this:
WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter
0xa934c0 pid: 3561 (default app)
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI master process (pid: 3561)
spawned uWSGI worker 1 (pid: 3575, cores: 4)
spawned uWSGI worker 2 (pid: 3576, cores: 4)
spawned uWSGI worker 3 (pid: 3583, cores: 4)
spawned uWSGI worker 4 (pid: 3587, cores: 4)
spawned uWSGI worker 5 (pid: 3591, cores: 4)
spawned uWSGI worker 6 (pid: 3595, cores: 4)
spawned uWSGI worker 7 (pid: 3599, cores: 4)
spawned uWSGI worker 8 (pid: 3603, cores: 4)
spawned uWSGI worker 9 (pid: 3607, cores: 4)
spawned uWSGI worker 10 (pid: 3611, cores: 4)
*** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
...so no traceback this time!
Then, browsing to localhost redirects to https://localhost and finally returns:
"Internal Server Error Galaxy was unable to successfully complete
your request An error occurred. This may be an intermittent problem
due to load or other
unpredictable factors, reloading the page may address the problem. The
error has been logged to our team."
That request was logged to uwsgi.log:
127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 -
"-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101
Firefox/35.0"
Error - : 'SCRIPT_NAME'
URL: https://localhost/
File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 159 in handle_request
trans = self.transaction_factory( environ )
File 'lib/galaxy/web/framework/webapp.py', line 71 in
self.set_transaction_factory( lambda e:
self.transaction_chooser( e, galaxy_app, session_cookie ) )
File 'lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__
self._ensure_logged_in_user( environ, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 441 in
_ensure_logged_in_user
if self.request.path.startswith( external_display_path ):
File 'lib/galaxy/web/framework/base.py', line 258 in __get__
value = self.func( obj )
File 'lib/galaxy/web/framework/base.py', line 341 in path
return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO']
KeyError: 'SCRIPT_NAME'
CGI Variables
-
DOCUMENT_ROOT: '/usr/share/nginx/html'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_HOST: 'localhost'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:35.0) Gecko/20100101 Firefox/35.0'
PATH_INFO: '/'
REMOTE_ADDR: '127.0.0.1'
REMOTE_PORT: '50064'
REQUEST_METHOD: 'GET'
REQUEST_URI: '/'
SERVER_NAME: 'localhost'
SERVER_PORT: '443'
SERVER_PROTOCOL: 'HTTP/1.1'
UWSGI_SCHEME: 'https'
WSGI Variables
--
application:
is_api_request: False
paste.cookies: (, '')
paste.expected_exceptions: []
paste.httpexceptions:
paste.recursive.forward:
paste.recursive.include:
paste.recursive.include_app_iter:
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'fadecee2abdd11e4bfb614feb5e02dd6'
uwsgi.core: 0
uwsgi.node: 'i changed this string to hide the server name'
uwsgi.version: '2.0.9'
wsgi process: 'Multi process AND threads (?)'
wsgi.file_wrapper:
[pid: 3607|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes}
[Tue Feb 3 14:51:01 2015] GET / => generated 777 bytes in 230 msecs
(HTTP/1.1 500) 1 headers in 63 bytes (1 switches on core 0)
I thought I would include some pieces of universe_wsgi.ini to help
with troubleshooting:
# HTTP Server
--
# Configuration of the internal HTTP server.
[server:main]
# The internal HTTP server to
Re: [galaxy-dev] Starting uWSGI
Hi Nate,
So I went ahead and set `static_enabled = False` in universe_wsgi.ini,
restarted uWSGI, and browsed to localhost. I'm including the results
of each step below:
After restarting uWSGI, the last few lines of uwsgi.log looked like this:
WSGI app 0 (mountpoint='') ready in 11 seconds on interpreter
0xa934c0 pid: 3561 (default app)
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI master process (pid: 3561)
spawned uWSGI worker 1 (pid: 3575, cores: 4)
spawned uWSGI worker 2 (pid: 3576, cores: 4)
spawned uWSGI worker 3 (pid: 3583, cores: 4)
spawned uWSGI worker 4 (pid: 3587, cores: 4)
spawned uWSGI worker 5 (pid: 3591, cores: 4)
spawned uWSGI worker 6 (pid: 3595, cores: 4)
spawned uWSGI worker 7 (pid: 3599, cores: 4)
spawned uWSGI worker 8 (pid: 3603, cores: 4)
spawned uWSGI worker 9 (pid: 3607, cores: 4)
spawned uWSGI worker 10 (pid: 3611, cores: 4)
*** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
...so no traceback this time!
Then, browsing to localhost redirects to https://localhost and finally returns:
"Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other
unpredictable factors, reloading the page may address the problem.
The error has been logged to our team."
That request was logged to uwsgi.log:
127.0.0.1 - - [03/Feb/2015:14:51:01 -0400] "GET / HTTP/1.1" 500 -
"-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:35.0) Gecko/20100101
Firefox/35.0"
Error - : 'SCRIPT_NAME'
URL: https://localhost/
File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 159 in handle_request
trans = self.transaction_factory( environ )
File 'lib/galaxy/web/framework/webapp.py', line 71 in
self.set_transaction_factory( lambda e:
self.transaction_chooser( e, galaxy_app, session_cookie ) )
File 'lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 207 in __init__
self._ensure_logged_in_user( environ, session_cookie )
File 'lib/galaxy/web/framework/webapp.py', line 441 in
_ensure_logged_in_user
if self.request.path.startswith( external_display_path ):
File 'lib/galaxy/web/framework/base.py', line 258 in __get__
value = self.func( obj )
File 'lib/galaxy/web/framework/base.py', line 341 in path
return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO']
KeyError: 'SCRIPT_NAME'
CGI Variables
-
DOCUMENT_ROOT: '/usr/share/nginx/html'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_HOST: 'localhost'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:35.0) Gecko/20100101 Firefox/35.0'
PATH_INFO: '/'
REMOTE_ADDR: '127.0.0.1'
REMOTE_PORT: '50064'
REQUEST_METHOD: 'GET'
REQUEST_URI: '/'
SERVER_NAME: 'localhost'
SERVER_PORT: '443'
SERVER_PROTOCOL: 'HTTP/1.1'
UWSGI_SCHEME: 'https'
WSGI Variables
--
application:
is_api_request: False
paste.cookies: (, '')
paste.expected_exceptions: []
paste.httpexceptions:
paste.recursive.forward:
paste.recursive.include:
paste.recursive.include_app_iter:
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'fadecee2abdd11e4bfb614feb5e02dd6'
uwsgi.core: 0
uwsgi.node: 'i changed this string to hide the server name'
uwsgi.version: '2.0.9'
wsgi process: 'Multi process AND threads (?)'
wsgi.file_wrapper:
[pid: 3607|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes}
[Tue Feb 3 14:51:01 2015] GET / => generated 777 bytes in 230 msecs
(HTTP/1.1 500) 1 headers in 63 bytes (1 switches on core 0)
I thought I would include some pieces of universe_wsgi.ini to help
with troubleshooting:
# HTTP Server
--
# Configuration of the internal HTTP server.
[server:main]
# The inter
Re: [galaxy-dev] Starting uWSGI
Hi Nicholas,
Set `static_enabled = False` in universe_wsgi.ini and restart uWSGI, and
see if that makes a difference.
Thanks,
--nate
On Mon, Feb 2, 2015 at 11:26 AM, Nicholas Kline wrote:
> Hi Nate. Thanks a lot for all the help so far. So, I started uWSGI like so:
>
> - activate virtual env
> - cd ~/galaxy-dist
> - PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
> universe_wsgi.ini
>
> Then browsed to localhost, which redirected to https://localhost/ as
> expected since I want all traffic to be over HTTPS, and finally
> returned:
>
> 502 Bad Gateway
>
> I checked uwsgi.log and it's quite large, almost 3,000 lines. Should I
> post it to this list for review? I've included the last few lines
> below:
>
> *** uWSGI is running in multiple interpreter mode ***
> spawned uWSGI master process (pid: 4083)
> spawned uWSGI worker 1 (pid: 4195, cores: 4)
> spawned uWSGI worker 2 (pid: 4199, cores: 4)
> spawned uWSGI worker 3 (pid: 4203, cores: 4)
> spawned uWSGI worker 4 (pid: 4207, cores: 4)
> spawned uWSGI worker 5 (pid: 4211, cores: 4)
> spawned uWSGI worker 6 (pid: 4215, cores: 4)
> spawned uWSGI worker 7 (pid: 4219, cores: 4)
> spawned uWSGI worker 8 (pid: 4223, cores: 4)
> spawned uWSGI worker 9 (pid: 4224, cores: 4)
> spawned uWSGI worker 10 (pid: 4225, cores: 4)
> *** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
> Traceback (most recent call last):
> File
> "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/urlmap.py",
> line 201, in __call__
> environ['SCRIPT_NAME'] += app_url
> KeyError: 'SCRIPT_NAME'
> [pid: 4219|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes} [Fri
> Jan 30 15:15:10 2015] GET / => generated 0 bytes in 18 msecs (HTTP/1.1
> 500) 0 headers in 0 bytes (0 switches on core 0)
>
> If you need me to post my Nginx config too, just let me know. Thanks!
>
>
>
> On Wed, Jan 28, 2015 at 2:53 PM, Nate Coraor wrote:
> > On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline wrote:
> >>
> >> Hi Nate. Thank you for the reply. So I installed uWSGI inside my
> >> Python virtual environment since that was one of the options listed in
> >> the documentation, like so:
> >>
> >> cd ~/galaxy_env/
> >> source bin/activate
> >> pip install uwsgi
> >>
> >> It looks like uWSGI was successfully installed. I then
> >> exited/deactivated the virtual environment via 'deactivate'.
> >>
> >> Next, I tried to start uWSGI:
> >>
> >> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
> >> --ini-paste config/galaxy.ini
> >
> >
> > Calling uwsgi after deactivating the virtualenv means it'd be running
> from
> > wherever it's found on $PATH, which is probably not the one you just
> > installed into the virtualenv. But if it works, it may not matter.
> >
> >>
> >>
> >> ... but it returned this:
> >>
> >>
> >> realpath() of config/galaxy.ini failed: No such file or directory
> >> [core/utils.c line 3607]
> >>
> >> So, I pointed it to universe_wsgi.ini instead, like so:
> >>
> >> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
> >> --ini-paste universe_wsgi.ini
> >
> >
> > universe_wsgi.ini was renamed to config/galaxy.ini late last year.
> However,
> > if you still have it, it's perfectly fine to leave it there and continue
> > using it.
> >
> >>
> >>
> >> ...and this was returned:
> >>
> >> [uWSGI] getting INI configuration from universe_wsgi.ini
> >>
> >> At that point, Terminal just kinda sits there and does not display any
> >> output, error messages, etc.
> >
> >
> > If uwsgi is running, this suggests it's working. If you have set up the
> > uwsgi proxy in nginx you should be able to try to access Galaxy via the
> web
> > at this point. More detail may be available in the uwsgi log file - did
> you
> > set `logto` in the `[uwsgi]` section of universe_wsgi.ini?
> >
> >>
> >> Questions:
> >>
> >> 1. Was I correct in specifying universe_wsgi.ini ?
> >
> >
> > The location of the config file is up to you. universe_wsgi.ini in the
> root
> > of the Galaxy directory was the old default.
> >
> >>
> >> 2. Nothing is returned after "[uWSGI] getting INI configuration from
> >> universe_wsgi.ini". Is that normal?
> >
> >
> > Yes. You probably want to set `logto` as described above and start uwsgi
> in
> > the background, e.g. with the `-d` command line option.
> >
> >> 3. Should I activate the Python virtual environment first (via "source
> >> bin/activate") before executing "~/galaxy-dist$
> >> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
> >> universe_wsgi.ini" ?
> >
> >
> > Yes, I would do this.
> >
> >>
> >> 4. Is the next step to start Galaxy, like so?
> >>
> >> cd galaxy-dist
> >> GALAXY_RUN_ALL=1 sh run.sh --daemon
> >
> >
> > uwsgi is running your Galaxy web processes, so I would check to ensure
> they
> > are working first. Once you've verified that, you can use the command
> above
> > to start any job handlers you have configured.
> >
> > --nate
> >
> >>
> >>
> >> I appreciate your help.
> >
Re: [galaxy-dev] Starting uWSGI
Hi Nate. Thanks a lot for all the help so far. So, I started uWSGI like so:
- activate virtual env
- cd ~/galaxy-dist
- PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
universe_wsgi.ini
Then browsed to localhost, which redirected to https://localhost/ as
expected since I want all traffic to be over HTTPS, and finally
returned:
502 Bad Gateway
I checked uwsgi.log and it's quite large, almost 3,000 lines. Should I
post it to this list for review? I've included the last few lines
below:
*** uWSGI is running in multiple interpreter mode ***
spawned uWSGI master process (pid: 4083)
spawned uWSGI worker 1 (pid: 4195, cores: 4)
spawned uWSGI worker 2 (pid: 4199, cores: 4)
spawned uWSGI worker 3 (pid: 4203, cores: 4)
spawned uWSGI worker 4 (pid: 4207, cores: 4)
spawned uWSGI worker 5 (pid: 4211, cores: 4)
spawned uWSGI worker 6 (pid: 4215, cores: 4)
spawned uWSGI worker 7 (pid: 4219, cores: 4)
spawned uWSGI worker 8 (pid: 4223, cores: 4)
spawned uWSGI worker 9 (pid: 4224, cores: 4)
spawned uWSGI worker 10 (pid: 4225, cores: 4)
*** Stats server enabled on 127.0.0.1:9191 fd: 30 ***
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/urlmap.py",
line 201, in __call__
environ['SCRIPT_NAME'] += app_url
KeyError: 'SCRIPT_NAME'
[pid: 4219|app: 0|req: 1/1] 127.0.0.1 () {40 vars in 593 bytes} [Fri
Jan 30 15:15:10 2015] GET / => generated 0 bytes in 18 msecs (HTTP/1.1
500) 0 headers in 0 bytes (0 switches on core 0)
If you need me to post my Nginx config too, just let me know. Thanks!
On Wed, Jan 28, 2015 at 2:53 PM, Nate Coraor wrote:
> On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline wrote:
>>
>> Hi Nate. Thank you for the reply. So I installed uWSGI inside my
>> Python virtual environment since that was one of the options listed in
>> the documentation, like so:
>>
>> cd ~/galaxy_env/
>> source bin/activate
>> pip install uwsgi
>>
>> It looks like uWSGI was successfully installed. I then
>> exited/deactivated the virtual environment via 'deactivate'.
>>
>> Next, I tried to start uWSGI:
>>
>> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
>> --ini-paste config/galaxy.ini
>
>
> Calling uwsgi after deactivating the virtualenv means it'd be running from
> wherever it's found on $PATH, which is probably not the one you just
> installed into the virtualenv. But if it works, it may not matter.
>
>>
>>
>> ... but it returned this:
>>
>>
>> realpath() of config/galaxy.ini failed: No such file or directory
>> [core/utils.c line 3607]
>>
>> So, I pointed it to universe_wsgi.ini instead, like so:
>>
>> ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi
>> --ini-paste universe_wsgi.ini
>
>
> universe_wsgi.ini was renamed to config/galaxy.ini late last year. However,
> if you still have it, it's perfectly fine to leave it there and continue
> using it.
>
>>
>>
>> ...and this was returned:
>>
>> [uWSGI] getting INI configuration from universe_wsgi.ini
>>
>> At that point, Terminal just kinda sits there and does not display any
>> output, error messages, etc.
>
>
> If uwsgi is running, this suggests it's working. If you have set up the
> uwsgi proxy in nginx you should be able to try to access Galaxy via the web
> at this point. More detail may be available in the uwsgi log file - did you
> set `logto` in the `[uwsgi]` section of universe_wsgi.ini?
>
>>
>> Questions:
>>
>> 1. Was I correct in specifying universe_wsgi.ini ?
>
>
> The location of the config file is up to you. universe_wsgi.ini in the root
> of the Galaxy directory was the old default.
>
>>
>> 2. Nothing is returned after "[uWSGI] getting INI configuration from
>> universe_wsgi.ini". Is that normal?
>
>
> Yes. You probably want to set `logto` as described above and start uwsgi in
> the background, e.g. with the `-d` command line option.
>
>> 3. Should I activate the Python virtual environment first (via "source
>> bin/activate") before executing "~/galaxy-dist$
>> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste
>> universe_wsgi.ini" ?
>
>
> Yes, I would do this.
>
>>
>> 4. Is the next step to start Galaxy, like so?
>>
>> cd galaxy-dist
>> GALAXY_RUN_ALL=1 sh run.sh --daemon
>
>
> uwsgi is running your Galaxy web processes, so I would check to ensure they
> are working first. Once you've verified that, you can use the command above
> to start any job handlers you have configured.
>
> --nate
>
>>
>>
>> I appreciate your help.
>>
>>
>>
>>
>> On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor wrote:
>> > Hi Nicholas,
>> >
>> > Sorry for the somewhat misleading text in the documentation. The part
>> > about
>> > "no extra modules or recompiling" refers to nginx itself - uWSGI
>> > protocol
>> > support is built in to the core functionality of nginx. This does not
>> > mean
>> > that uWSGI itself is installed. Installing uWSGI is addressed a bit
>> > further
>> > up:
>> >
>> >> You will also need to have uWSGI in
Re: [galaxy-dev] Starting uWSGI
On Wed, Jan 28, 2015 at 11:55 AM, Nicholas Kline wrote: > Hi Nate. Thank you for the reply. So I installed uWSGI inside my > Python virtual environment since that was one of the options listed in > the documentation, like so: > > cd ~/galaxy_env/ > source bin/activate > pip install uwsgi > > It looks like uWSGI was successfully installed. I then > exited/deactivated the virtual environment via 'deactivate'. > > Next, I tried to start uWSGI: > > ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi > --ini-paste config/galaxy.ini > Calling uwsgi after deactivating the virtualenv means it'd be running from wherever it's found on $PATH, which is probably not the one you just installed into the virtualenv. But if it works, it may not matter. > > ... but it returned this: > realpath() of config/galaxy.ini failed: No such file or directory > [core/utils.c line 3607] > > So, I pointed it to universe_wsgi.ini instead, like so: > > ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi > --ini-paste universe_wsgi.ini > universe_wsgi.ini was renamed to config/galaxy.ini late last year. However, if you still have it, it's perfectly fine to leave it there and continue using it. > > ...and this was returned: > > [uWSGI] getting INI configuration from universe_wsgi.ini > > At that point, Terminal just kinda sits there and does not display any > output, error messages, etc. > If uwsgi is running, this suggests it's working. If you have set up the uwsgi proxy in nginx you should be able to try to access Galaxy via the web at this point. More detail may be available in the uwsgi log file - did you set `logto` in the `[uwsgi]` section of universe_wsgi.ini? > Questions: > > 1. Was I correct in specifying universe_wsgi.ini ? > The location of the config file is up to you. universe_wsgi.ini in the root of the Galaxy directory was the old default. > 2. Nothing is returned after "[uWSGI] getting INI configuration from > universe_wsgi.ini". Is that normal? > Yes. You probably want to set `logto` as described above and start uwsgi in the background, e.g. with the `-d` command line option. 3. Should I activate the Python virtual environment first (via "source > bin/activate") before executing "~/galaxy-dist$ > PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste > universe_wsgi.ini" ? > Yes, I would do this. > 4. Is the next step to start Galaxy, like so? > > cd galaxy-dist > GALAXY_RUN_ALL=1 sh run.sh --daemon > uwsgi is running your Galaxy web processes, so I would check to ensure they are working first. Once you've verified that, you can use the command above to start any job handlers you have configured. --nate > > I appreciate your help. > > > > > On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor wrote: > > Hi Nicholas, > > > > Sorry for the somewhat misleading text in the documentation. The part > about > > "no extra modules or recompiling" refers to nginx itself - uWSGI protocol > > support is built in to the core functionality of nginx. This does not > mean > > that uWSGI itself is installed. Installing uWSGI is addressed a bit > further > > up: > > > >> You will also need to have uWSGI installed. There are a variety of ways > to > >> do this. It can be installed system-wide by installing from your > system's > >> package manager (on Debian and Ubuntu systems, the uwsgi and > >> uwsgi-plugin-python provide the necessary components), or with > >> theeasy_install or pip commands (which will install it to the system's > >> Python site-packages directory). Alternatively, if you are already > running > >> Galaxy from a Python virtualenv, you can use pip install uwsgi with that > >> virtualenv's copy of pip to install to that virtualenv as your > unprivileged > >> Galaxy user. > > > > > > In the case of Ubuntu sudo apt-get install uwsgi uwsgi-plugin-python > should > > provide the necessary components. > > > > --nate > > > > On Mon, Jan 26, 2015 at 2:46 PM, Nicholas Kline wrote: > >> > >> Hello, > >> > >> I am trying to setup a local production Galaxy server for our > >> department. Our Galaxy server environment is as follows: > >> > >> - Ubuntu 14.04 64-bit > >> - 94 GB Memory > >> - Intel Xeon > >> - Python virtual environment > >> - Nginx > >> - PostgreSQL > >> - ProFTPd > >> > >> Today I tried starting the Galaxy server for the first time. I think > >> the first step in that process is starting uWSGI, correct? To do so, I > >> executed these commands: > >> > >> cd ~/galaxy-dist/ > >> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste > >> config/galaxy.ini > >> > >> However, it appears something failed. This information is returned: > >> > >> The program 'uwsgi' can be found in the following packages: > >> * uwsgi-core > >> * uwsgi-plugin-alarm-curl > >> * uwsgi-plugin-alarm-xmpp > >> * uwsgi-plugin-curl-cron > >> * uwsgi-plugin-emperor-pg > >> * uwsgi-plugin-erlang > >> * uwsgi-plugin-geoip > >> * uwsgi-plugin-graylog2 > >>
Re: [galaxy-dev] Starting uWSGI
Hi Nate. Thank you for the reply. So I installed uWSGI inside my Python virtual environment since that was one of the options listed in the documentation, like so: cd ~/galaxy_env/ source bin/activate pip install uwsgi It looks like uWSGI was successfully installed. I then exited/deactivated the virtual environment via 'deactivate'. Next, I tried to start uWSGI: ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste config/galaxy.ini ... but it returned this: realpath() of config/galaxy.ini failed: No such file or directory [core/utils.c line 3607] So, I pointed it to universe_wsgi.ini instead, like so: ~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste universe_wsgi.ini ...and this was returned: [uWSGI] getting INI configuration from universe_wsgi.ini At that point, Terminal just kinda sits there and does not display any output, error messages, etc. Questions: 1. Was I correct in specifying universe_wsgi.ini ? 2. Nothing is returned after "[uWSGI] getting INI configuration from universe_wsgi.ini". Is that normal? 3. Should I activate the Python virtual environment first (via "source bin/activate") before executing "~/galaxy-dist$ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste universe_wsgi.ini" ? 4. Is the next step to start Galaxy, like so? cd galaxy-dist GALAXY_RUN_ALL=1 sh run.sh --daemon I appreciate your help. On Mon, Jan 26, 2015 at 5:22 PM, Nate Coraor wrote: > Hi Nicholas, > > Sorry for the somewhat misleading text in the documentation. The part about > "no extra modules or recompiling" refers to nginx itself - uWSGI protocol > support is built in to the core functionality of nginx. This does not mean > that uWSGI itself is installed. Installing uWSGI is addressed a bit further > up: > >> You will also need to have uWSGI installed. There are a variety of ways to >> do this. It can be installed system-wide by installing from your system's >> package manager (on Debian and Ubuntu systems, the uwsgi and >> uwsgi-plugin-python provide the necessary components), or with >> theeasy_install or pip commands (which will install it to the system's >> Python site-packages directory). Alternatively, if you are already running >> Galaxy from a Python virtualenv, you can use pip install uwsgi with that >> virtualenv's copy of pip to install to that virtualenv as your unprivileged >> Galaxy user. > > > In the case of Ubuntu sudo apt-get install uwsgi uwsgi-plugin-python should > provide the necessary components. > > --nate > > On Mon, Jan 26, 2015 at 2:46 PM, Nicholas Kline wrote: >> >> Hello, >> >> I am trying to setup a local production Galaxy server for our >> department. Our Galaxy server environment is as follows: >> >> - Ubuntu 14.04 64-bit >> - 94 GB Memory >> - Intel Xeon >> - Python virtual environment >> - Nginx >> - PostgreSQL >> - ProFTPd >> >> Today I tried starting the Galaxy server for the first time. I think >> the first step in that process is starting uWSGI, correct? To do so, I >> executed these commands: >> >> cd ~/galaxy-dist/ >> PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste >> config/galaxy.ini >> >> However, it appears something failed. This information is returned: >> >> The program 'uwsgi' can be found in the following packages: >> * uwsgi-core >> * uwsgi-plugin-alarm-curl >> * uwsgi-plugin-alarm-xmpp >> * uwsgi-plugin-curl-cron >> * uwsgi-plugin-emperor-pg >> * uwsgi-plugin-erlang >> * uwsgi-plugin-geoip >> * uwsgi-plugin-graylog2 >> * uwsgi-plugin-jvm-openjdk-6 >> * uwsgi-plugin-jvm-openjdk-7 >> * uwsgi-plugin-ldap >> * uwsgi-plugin-lua5.1 >> * uwsgi-plugin-lua5.2 >> * uwsgi-plugin-php >> * uwsgi-plugin-psgi >> * uwsgi-plugin-python >> * uwsgi-plugin-python3 >> * uwsgi-plugin-rack-ruby1.9.1 >> * uwsgi-plugin-router-access >> * uwsgi-plugin-sqlite3 >> * uwsgi-plugin-v8 >> * uwsgi-plugin-xslt >> Ask your administrator to install one of them >> >> According to the galaxy documentation at >> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling , >> "uWSGI support is built in to nginx, so no extra modules or >> recompiling should be required". >> >> Also, should '--ini-paste config/galaxy.ini' really be configured like >> this instead: --ini-paste universe_wsgi.ini ? >> >> Thank you >> ___ >> 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/ > > ___ 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.galaxyproje
Re: [galaxy-dev] Starting uWSGI
Hi Nicholas, Sorry for the somewhat misleading text in the documentation. The part about "no extra modules or recompiling" refers to nginx itself - uWSGI protocol support is built in to the core functionality of nginx. This does not mean that uWSGI itself is installed. Installing uWSGI is addressed a bit further up: You will also need to have uWSGI installed. There are a variety of ways to > do this. It can be installed system-wide by installing from your system's > package manager (on Debian and Ubuntu systems, the uwsgi and > uwsgi-plugin-python provide the necessary components), or with the > easy_install or pip commands (which will install it to the system's > Python site-packages directory). Alternatively, if you are already > running Galaxy from a Python virtualenv, you can use pip install uwsgi with > that virtualenv's copy of pip to install to that virtualenv as your > unprivileged Galaxy user. In the case of Ubuntu sudo apt-get install uwsgi uwsgi-plugin-python should provide the necessary components. --nate On Mon, Jan 26, 2015 at 2:46 PM, Nicholas Kline wrote: > Hello, > > I am trying to setup a local production Galaxy server for our > department. Our Galaxy server environment is as follows: > > - Ubuntu 14.04 64-bit > - 94 GB Memory > - Intel Xeon > - Python virtual environment > - Nginx > - PostgreSQL > - ProFTPd > > Today I tried starting the Galaxy server for the first time. I think > the first step in that process is starting uWSGI, correct? To do so, I > executed these commands: > > cd ~/galaxy-dist/ > PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste > config/galaxy.ini > > However, it appears something failed. This information is returned: > > The program 'uwsgi' can be found in the following packages: > * uwsgi-core > * uwsgi-plugin-alarm-curl > * uwsgi-plugin-alarm-xmpp > * uwsgi-plugin-curl-cron > * uwsgi-plugin-emperor-pg > * uwsgi-plugin-erlang > * uwsgi-plugin-geoip > * uwsgi-plugin-graylog2 > * uwsgi-plugin-jvm-openjdk-6 > * uwsgi-plugin-jvm-openjdk-7 > * uwsgi-plugin-ldap > * uwsgi-plugin-lua5.1 > * uwsgi-plugin-lua5.2 > * uwsgi-plugin-php > * uwsgi-plugin-psgi > * uwsgi-plugin-python > * uwsgi-plugin-python3 > * uwsgi-plugin-rack-ruby1.9.1 > * uwsgi-plugin-router-access > * uwsgi-plugin-sqlite3 > * uwsgi-plugin-v8 > * uwsgi-plugin-xslt > Ask your administrator to install one of them > > According to the galaxy documentation at > https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling , > "uWSGI support is built in to nginx, so no extra modules or > recompiling should be required". > > Also, should '--ini-paste config/galaxy.ini' really be configured like > this instead: --ini-paste universe_wsgi.ini ? > > Thank you > ___ > 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/ ___ 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] Starting uWSGI
Hello, I am trying to setup a local production Galaxy server for our department. Our Galaxy server environment is as follows: - Ubuntu 14.04 64-bit - 94 GB Memory - Intel Xeon - Python virtual environment - Nginx - PostgreSQL - ProFTPd Today I tried starting the Galaxy server for the first time. I think the first step in that process is starting uWSGI, correct? To do so, I executed these commands: cd ~/galaxy-dist/ PYTHONPATH=eggs/PasteDeploy-1.5.0-py2.7.egg uwsgi --ini-paste config/galaxy.ini However, it appears something failed. This information is returned: The program 'uwsgi' can be found in the following packages: * uwsgi-core * uwsgi-plugin-alarm-curl * uwsgi-plugin-alarm-xmpp * uwsgi-plugin-curl-cron * uwsgi-plugin-emperor-pg * uwsgi-plugin-erlang * uwsgi-plugin-geoip * uwsgi-plugin-graylog2 * uwsgi-plugin-jvm-openjdk-6 * uwsgi-plugin-jvm-openjdk-7 * uwsgi-plugin-ldap * uwsgi-plugin-lua5.1 * uwsgi-plugin-lua5.2 * uwsgi-plugin-php * uwsgi-plugin-psgi * uwsgi-plugin-python * uwsgi-plugin-python3 * uwsgi-plugin-rack-ruby1.9.1 * uwsgi-plugin-router-access * uwsgi-plugin-sqlite3 * uwsgi-plugin-v8 * uwsgi-plugin-xslt Ask your administrator to install one of them According to the galaxy documentation at https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling , "uWSGI support is built in to nginx, so no extra modules or recompiling should be required". Also, should '--ini-paste config/galaxy.ini' really be configured like this instead: --ini-paste universe_wsgi.ini ? Thank you ___ 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/
