Running Galaxy through Apache

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Running Galaxy through Apache

Jeffrey Long
Hi folks,
I am wanting to run a galaxy instance and serve it at a location other than the webserver root, i.e. at  http://mymachine.com/galaxy rather than just at http://mymachine.

To do this, I've followed the instructions about proxying Galaxy through Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.  I'm pretty sure I've followed the instructions exactly.  I enabled the necessary apache proxy modules and then I added these lines to my apache.conf file:


RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /myplace/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

...and re-started the apache server without a problem (note: I also tried it commenting out everything but the first, second and last line in case there was an issue with the static stuff).

I then made sure the following lines were present and uncommented in my universe_wsgi.ini file

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

[app:main]
 
filter-with = proxy-prefix
cookie_path = /galaxy

I start up Galaxy.  And still, I can only reach it on http://mymachine:8080, not at http://mymachine/galaxy as I intend.

Any help would be appreciated!  Thanks!

-Jeff


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Re: Running Galaxy through Apache

Adam Brenner
Jeff,

How / Where did you add the apache changes? Are you using VirutalHosts
or ... ? Quick glance, everything appears correct. Its been a while
since I used Apache (switched everything to nginx) however I believe
if you want to setup a Reverse Proxy, you need to add / use the proxy
pass lines which does not appear in the Galaxy Wiki.

Something like this should work: (untested...)

<IfModule mod_proxy.c>
  ProxyRequests Off
  <Proxy *>
    AddDefaultCharset off
    Order Deny,Allow
    Deny from all
    Allow from *.ualberta.ca # Change / Remove as needed
  </Proxy>

  ProxyPass /galaxy http://localhost:8080/
  ProxyPassReverse /galaxy http://localhost:8080/
  # Line below is optional
  Redirect permanent /galaxy http://mymachine.com/galaxy

  ProxyVia On
</IfModule>


Let us know,
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:

> Hi folks,
> I am wanting to run a galaxy instance and serve it at a location other than
> the webserver root, i.e. at  http://mymachine.com/galaxy rather than just at
> http://mymachine.
>
> To do this, I've followed the instructions about proxying Galaxy through
> Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.  I'm
> pretty sure I've followed the instructions exactly.  I enabled the necessary
> apache proxy modules and then I added these lines to my apache.conf file:
>
>
> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
> ^/galaxy/static/style/(.*)
> /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
> ^/galaxy/static/scripts/(.*) /myplace/galaxy-dist/static/scripts/packed/$1
> [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt [L]
> RewriteRule ^/galaxy(.*) <a href="http://localhost:8080$1">http://localhost:8080$1 [P]
>
> ...and re-started the apache server without a problem (note: I also tried it
> commenting out everything but the first, second and last line in case there
> was an issue with the static stuff).
>
> I then made sure the following lines were present and uncommented in my
> universe_wsgi.ini file
>
> [filter:proxy-prefix]
> use = egg:PasteDeploy#prefix
> prefix = /galaxy
>
> [app:main]
>
> filter-with = proxy-prefix
> cookie_path = /galaxy
>
>
> I start up Galaxy.  And still, I can only reach it on http://mymachine:8080,
> not at http://mymachine/galaxy as I intend.
>
> Any help would be appreciated!  Thanks!
>
> -Jeff
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
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Re: Running Galaxy through Apache

Jeffrey Long
1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website?  Those are the only ones I changed.  I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me.

Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly.

Exception happened during processing of request from ('127.0.0.1', 47424)
Traceback (most recent call last):
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
    self.handle()
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
    BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
    self.handle_one_request()
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
    self.wsgi_execute()
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
    self.wsgi_start_response)
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__
    return self.app(environ, start_response)
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__
    path_info = self.normalize_url(path_info, False)[1]
  File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url
    or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url
AssertionError: URL fragments must start with / or http:// (you gave '.')

2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time?  I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour.

Thanks, I'll try to remember to 'reply-all' here!

-Jeff


On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <[hidden email]> wrote:
Hia Jeff,

I think this is related to the proxy settings in Galaxy (universe_wsgi.ini)

What is happening is that if you look at the source code for your
galaxy website, it is trying to load css/images from:
http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if
you visit that link it offers you a 404 not found. Make sure the proxy
settings in your universe_wsgi.ini is set correctly.

If it is, it could be that you need to setup proxies for the
subdirectories as well. If you look at the nginx guide here:
http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
you will notice that we provide alias for /static/*.

In terms of doing this in Apache, you may need to add more proxy pass
lines that correspond to the subdirectories in question.


Be sure to post back to the Galaxy listsrv so that future people may
benefit from this!
-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <[hidden email]> wrote:
> Hi Adam thanks for the response,
> I'm not using VirtualHosts.  I just copied the lines shown into
> /etc/apache2/apache.conf (this is on Ubuntu Linux).
>
> I copied the lines you list (with appropriate modification) into this same
> apache.conf.  That seems to work - as far as Apache goes!  However, when I
> load galaxy in a browser now, I get a bunch of gobbledigook (it looks like
> the frames aren't being built properly or something).  You can take a look;
> I've temporarily enabled the site to be world-viewable.
>
> http://trove.usask.ca/galaxy
>
> Thanks for your help!
>
> -Jeff
>
>
> On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <[hidden email]> wrote:
>>
>> Jeff,
>>
>> How / Where did you add the apache changes? Are you using VirutalHosts
>> or ... ? Quick glance, everything appears correct. Its been a while
>> since I used Apache (switched everything to nginx) however I believe
>> if you want to setup a Reverse Proxy, you need to add / use the proxy
>> pass lines which does not appear in the Galaxy Wiki.
>>
>> Something like this should work: (untested...)
>>
>> <IfModule mod_proxy.c>
>>   ProxyRequests Off
>>   <Proxy *>
>>     AddDefaultCharset off
>>     Order Deny,Allow
>>     Deny from all
>>     Allow from *.ualberta.ca # Change / Remove as needed
>>   </Proxy>
>>
>>   ProxyPass /galaxy http://localhost:8080/
>>   ProxyPassReverse /galaxy http://localhost:8080/
>>   # Line below is optional
>>   Redirect permanent /galaxy http://mymachine.com/galaxy
>>
>>   ProxyVia On
>> </IfModule>
>>
>>
>> Let us know,
>> -Adam
>>
>> --
>> Adam Brenner
>> Computer Science, Undergraduate Student
>> Donald Bren School of Information and Computer Sciences
>>
>> Research Computing Support
>> Office of Information Technology
>> http://www.oit.uci.edu/rcs/
>>
>> University of California, Irvine
>> www.ics.uci.edu/~aebrenne/
>> [hidden email]
>>
>>
>> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:
>> > Hi folks,
>> > I am wanting to run a galaxy instance and serve it at a location other
>> > than
>> > the webserver root, i.e. at  http://mymachine.com/galaxy rather than
>> > just at
>> > http://mymachine.
>> >
>> > To do this, I've followed the instructions about proxying Galaxy through
>> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.
>> > I'm
>> > pretty sure I've followed the instructions exactly.  I enabled the
>> > necessary
>> > apache proxy modules and then I added these lines to my apache.conf
>> > file:
>> >
>> >
>> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
>> > ^/galaxy/static/style/(.*)
>> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
>> > ^/galaxy/static/scripts/(.*)
>> > /myplace/galaxy-dist/static/scripts/packed/$1
>> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
>> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico
>> > [L]
>> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt
>> > [L]
>> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
>> >
>> > ...and re-started the apache server without a problem (note: I also
>> > tried it
>> > commenting out everything but the first, second and last line in case
>> > there
>> > was an issue with the static stuff).
>> >
>> > I then made sure the following lines were present and uncommented in my
>> > universe_wsgi.ini file
>> >
>> > [filter:proxy-prefix]
>> > use = egg:PasteDeploy#prefix
>> > prefix = /galaxy
>> >
>> > [app:main]
>> >
>> > filter-with = proxy-prefix
>> > cookie_path = /galaxy
>> >
>> >
>> > I start up Galaxy.  And still, I can only reach it on
>> > http://mymachine:8080,
>> > not at http://mymachine/galaxy as I intend.
>> >
>> > Any help would be appreciated!  Thanks!
>> >
>> > -Jeff
>> >
>> >
>> > ___________________________________________________________
>> > 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:
>> >   http://lists.bx.psu.edu/
>> >
>> > 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Running Galaxy through Apache

Nate Coraor (nate@bx.psu.edu)
On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:

> 1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website?  Those are the only ones I changed.  I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me.
>
> Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly.
>
> Exception happened during processing of request from ('127.0.0.1', 47424)
> Traceback (most recent call last):
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
>     self.handle()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
>     self.handle_one_request()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
>     self.wsgi_execute()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__
>     return self.app(environ, start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__
>     path_info = self.normalize_url(path_info, False)[1]
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url
>     or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url
> AssertionError: URL fragments must start with / or http:// (you gave '.')

Hi Jeff,

Does the Apache log give any indication of what path is being accessed?  You may also want to enable mod_rewrite's debug logging to make sure it's behaving correctly.

> 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time?  I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour.

You can exclude the static page rewrites for the purposes of getting it working.  Galaxy's internal HTTP server will serve the static pages itself.

--nate

>
> Thanks, I'll try to remember to 'reply-all' here!
>
> -Jeff
>
>
> On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <[hidden email]> wrote:
> Hia Jeff,
>
> I think this is related to the proxy settings in Galaxy (universe_wsgi.ini)
>
> What is happening is that if you look at the source code for your
> galaxy website, it is trying to load css/images from:
> http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if
> you visit that link it offers you a 404 not found. Make sure the proxy
> settings in your universe_wsgi.ini is set correctly.
>
> If it is, it could be that you need to setup proxies for the
> subdirectories as well. If you look at the nginx guide here:
> http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
> you will notice that we provide alias for /static/*.
>
> In terms of doing this in Apache, you may need to add more proxy pass
> lines that correspond to the subdirectories in question.
>
>
> Be sure to post back to the Galaxy listsrv so that future people may
> benefit from this!
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
>
>
> On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <[hidden email]> wrote:
> > Hi Adam thanks for the response,
> > I'm not using VirtualHosts.  I just copied the lines shown into
> > /etc/apache2/apache.conf (this is on Ubuntu Linux).
> >
> > I copied the lines you list (with appropriate modification) into this same
> > apache.conf.  That seems to work - as far as Apache goes!  However, when I
> > load galaxy in a browser now, I get a bunch of gobbledigook (it looks like
> > the frames aren't being built properly or something).  You can take a look;
> > I've temporarily enabled the site to be world-viewable.
> >
> > http://trove.usask.ca/galaxy
> >
> > Thanks for your help!
> >
> > -Jeff
> >
> >
> > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <[hidden email]> wrote:
> >>
> >> Jeff,
> >>
> >> How / Where did you add the apache changes? Are you using VirutalHosts
> >> or ... ? Quick glance, everything appears correct. Its been a while
> >> since I used Apache (switched everything to nginx) however I believe
> >> if you want to setup a Reverse Proxy, you need to add / use the proxy
> >> pass lines which does not appear in the Galaxy Wiki.
> >>
> >> Something like this should work: (untested...)
> >>
> >> <IfModule mod_proxy.c>
> >>   ProxyRequests Off
> >>   <Proxy *>
> >>     AddDefaultCharset off
> >>     Order Deny,Allow
> >>     Deny from all
> >>     Allow from *.ualberta.ca # Change / Remove as needed
> >>   </Proxy>
> >>
> >>   ProxyPass /galaxy http://localhost:8080/
> >>   ProxyPassReverse /galaxy http://localhost:8080/
> >>   # Line below is optional
> >>   Redirect permanent /galaxy http://mymachine.com/galaxy
> >>
> >>   ProxyVia On
> >> </IfModule>
> >>
> >>
> >> Let us know,
> >> -Adam
> >>
> >> --
> >> Adam Brenner
> >> Computer Science, Undergraduate Student
> >> Donald Bren School of Information and Computer Sciences
> >>
> >> Research Computing Support
> >> Office of Information Technology
> >> http://www.oit.uci.edu/rcs/
> >>
> >> University of California, Irvine
> >> www.ics.uci.edu/~aebrenne/
> >> [hidden email]
> >>
> >>
> >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:
> >> > Hi folks,
> >> > I am wanting to run a galaxy instance and serve it at a location other
> >> > than
> >> > the webserver root, i.e. at  http://mymachine.com/galaxy rather than
> >> > just at
> >> > http://mymachine.
> >> >
> >> > To do this, I've followed the instructions about proxying Galaxy through
> >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.
> >> > I'm
> >> > pretty sure I've followed the instructions exactly.  I enabled the
> >> > necessary
> >> > apache proxy modules and then I added these lines to my apache.conf
> >> > file:
> >> >
> >> >
> >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
> >> > ^/galaxy/static/style/(.*)
> >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
> >> > ^/galaxy/static/scripts/(.*)
> >> > /myplace/galaxy-dist/static/scripts/packed/$1
> >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
> >> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico
> >> > [L]
> >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt
> >> > [L]
> >> > RewriteRule ^/galaxy(.*) <a href="http://localhost:8080$1">http://localhost:8080$1 [P]
> >> >
> >> > ...and re-started the apache server without a problem (note: I also
> >> > tried it
> >> > commenting out everything but the first, second and last line in case
> >> > there
> >> > was an issue with the static stuff).
> >> >
> >> > I then made sure the following lines were present and uncommented in my
> >> > universe_wsgi.ini file
> >> >
> >> > [filter:proxy-prefix]
> >> > use = egg:PasteDeploy#prefix
> >> > prefix = /galaxy
> >> >
> >> > [app:main]
> >> >
> >> > filter-with = proxy-prefix
> >> > cookie_path = /galaxy
> >> >
> >> >
> >> > I start up Galaxy.  And still, I can only reach it on
> >> > http://mymachine:8080,
> >> > not at http://mymachine/galaxy as I intend.
> >> >
> >> > Any help would be appreciated!  Thanks!
> >> >
> >> > -Jeff
> >> >
> >> >
> >> > ___________________________________________________________
> >> > 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:
> >> >   http://lists.bx.psu.edu/
> >> >
> >> > 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Running Galaxy through Apache

Jeffrey Long
In the Apache access.log, a single access link results in a great many output lines; the first two look like this:

128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy HTTP/1.1" 200 5058 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"
128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy/static/style/base.css?v=1367440234 HTTP/1.1" 404 495 "http://trove.usask.ca/galaxy" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"

If I'm reading this right, the second one involves a 404 error.  Indeed, I don't see any static/style directory in my galaxy location...should there be one?

I don't get anything new in apache's error.log as a result of a single access attempt.

-Jeff



On Wed, May 1, 2013 at 6:16 AM, Nate Coraor <[hidden email]> wrote:
On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:

> 1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website?  Those are the only ones I changed.  I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me.
>
> Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly.
>
> Exception happened during processing of request from ('127.0.0.1', 47424)
> Traceback (most recent call last):
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
>     self.handle()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
>     self.handle_one_request()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
>     self.wsgi_execute()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__
>     return self.app(environ, start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__
>     path_info = self.normalize_url(path_info, False)[1]
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url
>     or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url
> AssertionError: URL fragments must start with / or http:// (you gave '.')

Hi Jeff,

Does the Apache log give any indication of what path is being accessed?  You may also want to enable mod_rewrite's debug logging to make sure it's behaving correctly.

> 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time?  I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour.

You can exclude the static page rewrites for the purposes of getting it working.  Galaxy's internal HTTP server will serve the static pages itself.

--nate

>
> Thanks, I'll try to remember to 'reply-all' here!
>
> -Jeff
>
>
> On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <[hidden email]> wrote:
> Hia Jeff,
>
> I think this is related to the proxy settings in Galaxy (universe_wsgi.ini)
>
> What is happening is that if you look at the source code for your
> galaxy website, it is trying to load css/images from:
> http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if
> you visit that link it offers you a 404 not found. Make sure the proxy
> settings in your universe_wsgi.ini is set correctly.
>
> If it is, it could be that you need to setup proxies for the
> subdirectories as well. If you look at the nginx guide here:
> http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
> you will notice that we provide alias for /static/*.
>
> In terms of doing this in Apache, you may need to add more proxy pass
> lines that correspond to the subdirectories in question.
>
>
> Be sure to post back to the Galaxy listsrv so that future people may
> benefit from this!
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
>
>
> On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <[hidden email]> wrote:
> > Hi Adam thanks for the response,
> > I'm not using VirtualHosts.  I just copied the lines shown into
> > /etc/apache2/apache.conf (this is on Ubuntu Linux).
> >
> > I copied the lines you list (with appropriate modification) into this same
> > apache.conf.  That seems to work - as far as Apache goes!  However, when I
> > load galaxy in a browser now, I get a bunch of gobbledigook (it looks like
> > the frames aren't being built properly or something).  You can take a look;
> > I've temporarily enabled the site to be world-viewable.
> >
> > http://trove.usask.ca/galaxy
> >
> > Thanks for your help!
> >
> > -Jeff
> >
> >
> > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <[hidden email]> wrote:
> >>
> >> Jeff,
> >>
> >> How / Where did you add the apache changes? Are you using VirutalHosts
> >> or ... ? Quick glance, everything appears correct. Its been a while
> >> since I used Apache (switched everything to nginx) however I believe
> >> if you want to setup a Reverse Proxy, you need to add / use the proxy
> >> pass lines which does not appear in the Galaxy Wiki.
> >>
> >> Something like this should work: (untested...)
> >>
> >> <IfModule mod_proxy.c>
> >>   ProxyRequests Off
> >>   <Proxy *>
> >>     AddDefaultCharset off
> >>     Order Deny,Allow
> >>     Deny from all
> >>     Allow from *.ualberta.ca # Change / Remove as needed
> >>   </Proxy>
> >>
> >>   ProxyPass /galaxy http://localhost:8080/
> >>   ProxyPassReverse /galaxy http://localhost:8080/
> >>   # Line below is optional
> >>   Redirect permanent /galaxy http://mymachine.com/galaxy
> >>
> >>   ProxyVia On
> >> </IfModule>
> >>
> >>
> >> Let us know,
> >> -Adam
> >>
> >> --
> >> Adam Brenner
> >> Computer Science, Undergraduate Student
> >> Donald Bren School of Information and Computer Sciences
> >>
> >> Research Computing Support
> >> Office of Information Technology
> >> http://www.oit.uci.edu/rcs/
> >>
> >> University of California, Irvine
> >> www.ics.uci.edu/~aebrenne/
> >> [hidden email]
> >>
> >>
> >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:
> >> > Hi folks,
> >> > I am wanting to run a galaxy instance and serve it at a location other
> >> > than
> >> > the webserver root, i.e. at  http://mymachine.com/galaxy rather than
> >> > just at
> >> > http://mymachine.
> >> >
> >> > To do this, I've followed the instructions about proxying Galaxy through
> >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.
> >> > I'm
> >> > pretty sure I've followed the instructions exactly.  I enabled the
> >> > necessary
> >> > apache proxy modules and then I added these lines to my apache.conf
> >> > file:
> >> >
> >> >
> >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
> >> > ^/galaxy/static/style/(.*)
> >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
> >> > ^/galaxy/static/scripts/(.*)
> >> > /myplace/galaxy-dist/static/scripts/packed/$1
> >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
> >> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico
> >> > [L]
> >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt
> >> > [L]
> >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
> >> >
> >> > ...and re-started the apache server without a problem (note: I also
> >> > tried it
> >> > commenting out everything but the first, second and last line in case
> >> > there
> >> > was an issue with the static stuff).
> >> >
> >> > I then made sure the following lines were present and uncommented in my
> >> > universe_wsgi.ini file
> >> >
> >> > [filter:proxy-prefix]
> >> > use = egg:PasteDeploy#prefix
> >> > prefix = /galaxy
> >> >
> >> > [app:main]
> >> >
> >> > filter-with = proxy-prefix
> >> > cookie_path = /galaxy
> >> >
> >> >
> >> > I start up Galaxy.  And still, I can only reach it on
> >> > http://mymachine:8080,
> >> > not at http://mymachine/galaxy as I intend.
> >> >
> >> > Any help would be appreciated!  Thanks!
> >> >
> >> > -Jeff
> >> >
> >> >
> >> > ___________________________________________________________
> >> > 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:
> >> >   http://lists.bx.psu.edu/
> >> >
> >> > 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Running Galaxy through Apache

Adam Brenner
Jeff,

Did you ever get this to work?

-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Wed, May 1, 2013 at 1:52 PM, Jeffrey Long <[hidden email]> wrote:
In the Apache access.log, a single access link results in a great many output lines; the first two look like this:

128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy HTTP/1.1" 200 5058 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"
128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy/static/style/base.css?v=1367440234 HTTP/1.1" 404 495 "http://trove.usask.ca/galaxy" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"

If I'm reading this right, the second one involves a 404 error.  Indeed, I don't see any static/style directory in my galaxy location...should there be one?

I don't get anything new in apache's error.log as a result of a single access attempt.

-Jeff



On Wed, May 1, 2013 at 6:16 AM, Nate Coraor <[hidden email]> wrote:
On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:

> 1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website?  Those are the only ones I changed.  I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me.
>
> Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly.
>
> Exception happened during processing of request from ('127.0.0.1', 47424)
> Traceback (most recent call last):
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
>     self.handle()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
>     self.handle_one_request()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
>     self.wsgi_execute()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__
>     return self.app(environ, start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__
>     path_info = self.normalize_url(path_info, False)[1]
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url
>     or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url
> AssertionError: URL fragments must start with / or http:// (you gave '.')

Hi Jeff,

Does the Apache log give any indication of what path is being accessed?  You may also want to enable mod_rewrite's debug logging to make sure it's behaving correctly.

> 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time?  I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour.

You can exclude the static page rewrites for the purposes of getting it working.  Galaxy's internal HTTP server will serve the static pages itself.

--nate

>
> Thanks, I'll try to remember to 'reply-all' here!
>
> -Jeff
>
>
> On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <[hidden email]> wrote:
> Hia Jeff,
>
> I think this is related to the proxy settings in Galaxy (universe_wsgi.ini)
>
> What is happening is that if you look at the source code for your
> galaxy website, it is trying to load css/images from:
> http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if
> you visit that link it offers you a 404 not found. Make sure the proxy
> settings in your universe_wsgi.ini is set correctly.
>
> If it is, it could be that you need to setup proxies for the
> subdirectories as well. If you look at the nginx guide here:
> http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
> you will notice that we provide alias for /static/*.
>
> In terms of doing this in Apache, you may need to add more proxy pass
> lines that correspond to the subdirectories in question.
>
>
> Be sure to post back to the Galaxy listsrv so that future people may
> benefit from this!
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
>
>
> On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <[hidden email]> wrote:
> > Hi Adam thanks for the response,
> > I'm not using VirtualHosts.  I just copied the lines shown into
> > /etc/apache2/apache.conf (this is on Ubuntu Linux).
> >
> > I copied the lines you list (with appropriate modification) into this same
> > apache.conf.  That seems to work - as far as Apache goes!  However, when I
> > load galaxy in a browser now, I get a bunch of gobbledigook (it looks like
> > the frames aren't being built properly or something).  You can take a look;
> > I've temporarily enabled the site to be world-viewable.
> >
> > http://trove.usask.ca/galaxy
> >
> > Thanks for your help!
> >
> > -Jeff
> >
> >
> > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <[hidden email]> wrote:
> >>
> >> Jeff,
> >>
> >> How / Where did you add the apache changes? Are you using VirutalHosts
> >> or ... ? Quick glance, everything appears correct. Its been a while
> >> since I used Apache (switched everything to nginx) however I believe
> >> if you want to setup a Reverse Proxy, you need to add / use the proxy
> >> pass lines which does not appear in the Galaxy Wiki.
> >>
> >> Something like this should work: (untested...)
> >>
> >> <IfModule mod_proxy.c>
> >>   ProxyRequests Off
> >>   <Proxy *>
> >>     AddDefaultCharset off
> >>     Order Deny,Allow
> >>     Deny from all
> >>     Allow from *.ualberta.ca # Change / Remove as needed
> >>   </Proxy>
> >>
> >>   ProxyPass /galaxy http://localhost:8080/
> >>   ProxyPassReverse /galaxy http://localhost:8080/
> >>   # Line below is optional
> >>   Redirect permanent /galaxy http://mymachine.com/galaxy
> >>
> >>   ProxyVia On
> >> </IfModule>
> >>
> >>
> >> Let us know,
> >> -Adam
> >>
> >> --
> >> Adam Brenner
> >> Computer Science, Undergraduate Student
> >> Donald Bren School of Information and Computer Sciences
> >>
> >> Research Computing Support
> >> Office of Information Technology
> >> http://www.oit.uci.edu/rcs/
> >>
> >> University of California, Irvine
> >> www.ics.uci.edu/~aebrenne/
> >> [hidden email]
> >>
> >>
> >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:
> >> > Hi folks,
> >> > I am wanting to run a galaxy instance and serve it at a location other
> >> > than
> >> > the webserver root, i.e. at  http://mymachine.com/galaxy rather than
> >> > just at
> >> > http://mymachine.
> >> >
> >> > To do this, I've followed the instructions about proxying Galaxy through
> >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.
> >> > I'm
> >> > pretty sure I've followed the instructions exactly.  I enabled the
> >> > necessary
> >> > apache proxy modules and then I added these lines to my apache.conf
> >> > file:
> >> >
> >> >
> >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
> >> > ^/galaxy/static/style/(.*)
> >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
> >> > ^/galaxy/static/scripts/(.*)
> >> > /myplace/galaxy-dist/static/scripts/packed/$1
> >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
> >> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico
> >> > [L]
> >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt
> >> > [L]
> >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
> >> >
> >> > ...and re-started the apache server without a problem (note: I also
> >> > tried it
> >> > commenting out everything but the first, second and last line in case
> >> > there
> >> > was an issue with the static stuff).
> >> >
> >> > I then made sure the following lines were present and uncommented in my
> >> > universe_wsgi.ini file
> >> >
> >> > [filter:proxy-prefix]
> >> > use = egg:PasteDeploy#prefix
> >> > prefix = /galaxy
> >> >
> >> > [app:main]
> >> >
> >> > filter-with = proxy-prefix
> >> > cookie_path = /galaxy
> >> >
> >> >
> >> > I start up Galaxy.  And still, I can only reach it on
> >> > http://mymachine:8080,
> >> > not at http://mymachine/galaxy as I intend.
> >> >
> >> > Any help would be appreciated!  Thanks!
> >> >
> >> > -Jeff
> >> >
> >> >
> >> > ___________________________________________________________
> >> > 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:
> >> >   http://lists.bx.psu.edu/
> >> >
> >> > 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Running Galaxy through Apache

Jeffrey Long
Hi guys, 
Yeah, thanks for the help.  It just one more tweak to the apache2.conf configuration.

I had to change
  {{{
   ProxyPass /galaxy http://localhost:8080
   ProxyPassReverse /galaxy http://localhost:8080
 }}}
 to
 {{{
   ProxyPass /galaxy http://localhost:8080/galaxy
   ProxyPassReverse /galaxy http://localhost:8080/galaxy
 }}}

With that change, it seems to be up and running now.

-Jeff


On Sat, May 4, 2013 at 1:35 PM, Adam Brenner <[hidden email]> wrote:
Jeff,

Did you ever get this to work?

-Adam

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Wed, May 1, 2013 at 1:52 PM, Jeffrey Long <[hidden email]> wrote:
In the Apache access.log, a single access link results in a great many output lines; the first two look like this:

128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy HTTP/1.1" 200 5058 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"
128.233.109.35 - - [01/May/2013:14:31:29 -0600] "GET /galaxy/static/style/base.css?v=1367440234 HTTP/1.1" 404 495 "http://trove.usask.ca/galaxy" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.29.13 (KHTML, like Gecko) Version/6.0.4 Safari/536.29.13"

If I'm reading this right, the second one involves a 404 error.  Indeed, I don't see any static/style directory in my galaxy location...should there be one?

I don't get anything new in apache's error.log as a result of a single access attempt.

-Jeff



On Wed, May 1, 2013 at 6:16 AM, Nate Coraor <[hidden email]> wrote:
On Apr 30, 2013, at 5:15 PM, Jeffrey Long wrote:

> 1) Any idea which proxy settings in the universe_wsgi file need to be set other than the ones on the website?  Those are the only ones I changed.  I scrolled down to the 'Advanced Proxy' settings but didn't see anything that looked relevant to me.
>
> Probably I should have sent this earlier, but this is the traceback I get; it looks like there's a url somewhere that's not getting passed along or re-assembled properly.
>
> Exception happened during processing of request from ('127.0.0.1', 47424)
> Traceback (most recent call last):
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
>     self.handle()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
>     self.handle_one_request()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
>     self.wsgi_execute()
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 285, in __call__
>     return self.app(environ, start_response)
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 193, in __call__
>     path_info = self.normalize_url(path_info, False)[1]
>   File "/mnt2/birl/MAVEN/bin/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 117, in normalize_url
>     or self.domain_url_re.search(url)), "URL fragments must start with / or http:// (you gave %r)" % url
> AssertionError: URL fragments must start with / or http:// (you gave '.')

Hi Jeff,

Does the Apache log give any indication of what path is being accessed?  You may also want to enable mod_rewrite's debug logging to make sure it's behaving correctly.

> 2) Are the static subdirectories strictly necessary, or can I worry about one problem at a time?  I've tried both commenting out the proxy lines (in apache2.conf) and leaving them in, and I get the same behaviour.

You can exclude the static page rewrites for the purposes of getting it working.  Galaxy's internal HTTP server will serve the static pages itself.

--nate

>
> Thanks, I'll try to remember to 'reply-all' here!
>
> -Jeff
>
>
> On Mon, Apr 29, 2013 at 1:23 PM, Adam Brenner <[hidden email]> wrote:
> Hia Jeff,
>
> I think this is related to the proxy settings in Galaxy (universe_wsgi.ini)
>
> What is happening is that if you look at the source code for your
> galaxy website, it is trying to load css/images from:
> http://trove.usask.ca/galaxy/static/style/base.css?v=1367254127 But if
> you visit that link it offers you a 404 not found. Make sure the proxy
> settings in your universe_wsgi.ini is set correctly.
>
> If it is, it could be that you need to setup proxies for the
> subdirectories as well. If you look at the nginx guide here:
> http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
> you will notice that we provide alias for /static/*.
>
> In terms of doing this in Apache, you may need to add more proxy pass
> lines that correspond to the subdirectories in question.
>
>
> Be sure to post back to the Galaxy listsrv so that future people may
> benefit from this!
> -Adam
>
> --
> Adam Brenner
> Computer Science, Undergraduate Student
> Donald Bren School of Information and Computer Sciences
>
> Research Computing Support
> Office of Information Technology
> http://www.oit.uci.edu/rcs/
>
> University of California, Irvine
> www.ics.uci.edu/~aebrenne/
> [hidden email]
>
>
> On Mon, Apr 29, 2013 at 9:51 AM, Jeffrey Long <[hidden email]> wrote:
> > Hi Adam thanks for the response,
> > I'm not using VirtualHosts.  I just copied the lines shown into
> > /etc/apache2/apache.conf (this is on Ubuntu Linux).
> >
> > I copied the lines you list (with appropriate modification) into this same
> > apache.conf.  That seems to work - as far as Apache goes!  However, when I
> > load galaxy in a browser now, I get a bunch of gobbledigook (it looks like
> > the frames aren't being built properly or something).  You can take a look;
> > I've temporarily enabled the site to be world-viewable.
> >
> > http://trove.usask.ca/galaxy
> >
> > Thanks for your help!
> >
> > -Jeff
> >
> >
> > On Fri, Apr 26, 2013 at 10:11 PM, Adam Brenner <[hidden email]> wrote:
> >>
> >> Jeff,
> >>
> >> How / Where did you add the apache changes? Are you using VirutalHosts
> >> or ... ? Quick glance, everything appears correct. Its been a while
> >> since I used Apache (switched everything to nginx) however I believe
> >> if you want to setup a Reverse Proxy, you need to add / use the proxy
> >> pass lines which does not appear in the Galaxy Wiki.
> >>
> >> Something like this should work: (untested...)
> >>
> >> <IfModule mod_proxy.c>
> >>   ProxyRequests Off
> >>   <Proxy *>
> >>     AddDefaultCharset off
> >>     Order Deny,Allow
> >>     Deny from all
> >>     Allow from *.ualberta.ca # Change / Remove as needed
> >>   </Proxy>
> >>
> >>   ProxyPass /galaxy http://localhost:8080/
> >>   ProxyPassReverse /galaxy http://localhost:8080/
> >>   # Line below is optional
> >>   Redirect permanent /galaxy http://mymachine.com/galaxy
> >>
> >>   ProxyVia On
> >> </IfModule>
> >>
> >>
> >> Let us know,
> >> -Adam
> >>
> >> --
> >> Adam Brenner
> >> Computer Science, Undergraduate Student
> >> Donald Bren School of Information and Computer Sciences
> >>
> >> Research Computing Support
> >> Office of Information Technology
> >> http://www.oit.uci.edu/rcs/
> >>
> >> University of California, Irvine
> >> www.ics.uci.edu/~aebrenne/
> >> [hidden email]
> >>
> >>
> >> On Fri, Apr 26, 2013 at 2:56 PM, Jeffrey Long <[hidden email]> wrote:
> >> > Hi folks,
> >> > I am wanting to run a galaxy instance and serve it at a location other
> >> > than
> >> > the webserver root, i.e. at  http://mymachine.com/galaxy rather than
> >> > just at
> >> > http://mymachine.
> >> >
> >> > To do this, I've followed the instructions about proxying Galaxy through
> >> > Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy.
> >> > I'm
> >> > pretty sure I've followed the instructions exactly.  I enabled the
> >> > necessary
> >> > apache proxy modules and then I added these lines to my apache.conf
> >> > file:
> >> >
> >> >
> >> > RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule
> >> > ^/galaxy/static/style/(.*)
> >> > /myplace/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule
> >> > ^/galaxy/static/scripts/(.*)
> >> > /myplace/galaxy-dist/static/scripts/packed/$1
> >> > [L] RewriteRule ^/galaxy/static/(.*) /myplace/galaxy-dist/static/$1 [L]
> >> > RewriteRule ^/galaxy/favicon.ico /myplace/galaxy-dist/static/favicon.ico
> >> > [L]
> >> > RewriteRule ^/galaxy/robots.txt /myplace/galaxy-dist/static/robots.txt
> >> > [L]
> >> > RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
> >> >
> >> > ...and re-started the apache server without a problem (note: I also
> >> > tried it
> >> > commenting out everything but the first, second and last line in case
> >> > there
> >> > was an issue with the static stuff).
> >> >
> >> > I then made sure the following lines were present and uncommented in my
> >> > universe_wsgi.ini file
> >> >
> >> > [filter:proxy-prefix]
> >> > use = egg:PasteDeploy#prefix
> >> > prefix = /galaxy
> >> >
> >> > [app:main]
> >> >
> >> > filter-with = proxy-prefix
> >> > cookie_path = /galaxy
> >> >
> >> >
> >> > I start up Galaxy.  And still, I can only reach it on
> >> > http://mymachine:8080,
> >> > not at http://mymachine/galaxy as I intend.
> >> >
> >> > Any help would be appreciated!  Thanks!
> >> >
> >> > -Jeff
> >> >
> >> >
> >> > ___________________________________________________________
> >> > 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:
> >> >   http://lists.bx.psu.edu/
> >> >
> >> > 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:
>  http://lists.bx.psu.edu/
>
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___________________________________________________________
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