Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-10 Thread Makis Ladoukakis

Hello thank you for your reply.

I followed the instructions on your blog together with the Galaxy tutorial and 
even though I changed the port to 127.0.0.1:8091 in supervisord.conf it refuses 
the connection:

supervisorctl status   
http://localhost:9001 refused connection

The port is the wrong one as well!!! It was 8091 the port that I used

ps ax |grep uwsgi doesn't display a working uwsgi service

and sudo lsof -i :4001 returns nothing.

My supervisord.conf file is the following:

[inet_http_server]
port=127.0.0.1:8091

[supervisord]

[supervisorctl]

[program:galaxy_uwsgi]
command = /usr/bin/uwsgi --plugin python --ini-paste 
/home/galaxy/galaxy/config/galaxy.ini
directory   = /home/galaxy/galaxy
umask   = 022
autostart   = true
autorestart = true
startsecs   = 10
user= galaxy
environment = 
PATH=/home/galaxy/galaxy_env:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs,PYTHONPATH=/home/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg
numprocs= 1
stopsignal  = INT

[program:handler]
command = /home/galaxy/galaxy_env/bin/python ./scripts/paster.py serve 
config/galaxy.ini --server-name=handler%(process_num)s 
--pid-file=/home/galaxy/galaxy/handler%(process_num)s.pid 
--log-file=/home/galaxy/galaxy/handler%(process_num)s.log
directory   = /home/galaxy/galaxy
process_name= handler%(process_num)s
numprocs= 8
umask   = 022
autostart   = true
autorestart = true
startsecs   = 15
user= galaxy
environment = PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs
#I didn't include SGE_root as i don't have sge installed

[group:galaxy]
programs = handler, galaxy_uwsgi



Can you help me please?

What am I missing?

Thank you,
Makis


Date: Fri, 4 Dec 2015 17:57:38 +0200
Subject: RE: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

I've written up my experiences in a 
blog:http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/The only 
Galaxy side changes were the ones mentioned on the Scaling page. The Bad 
Gateway message means that Apache can't talk to the uWSGI so what is the state 
of uWSGI?
Are you using supervisord? Does supervisorctl show the uWSGI process running? 
Does ps ax |grep uwsgi show it running? What does sudo lsof -i :4001 show is 
listening on port 4001? That would be the starting point of my debugging.
Peter

On 4 Dec 2015 10:57, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



It is uwsgi that I am trying but with apache. Could you let me know what 
changes you made to the configuration of Galaxy?

Thank you,
Makis

Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hi Makis, I recently implemented something like this using uWSGI with a nginx 
frontend. Would you consider using uWSGI instead of your current approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static

Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-04 Thread Peter van Heusden
Hi Makis, I recently implemented something like this using uWSGI with a
nginx frontend. Would you consider using uWSGI instead of your current
approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:

> Sorry for bumping my own question but I didn't get any replies. Has anyone
> succesfully installed a production Galaxy instance?
>
> I could really use some advice.
>
> Thank you,
> Makis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
>
> Hello everyone,
>
> I am trying to setup a Galaxy instance for a multi-user production
> environment and I tried to follow the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh
> --daemon) I got the following error in my browser:Bad Gateway The proxy
> server received an invalid response from an upstream server.
>
>
> I don't get any errors from the paster.log files so I am guessing the
> error is somewhere in my apache configuration although I can't see where it
> could be.
>
>
> Has anyone encountered this problem before?
>
> Kind regards,
> Makis
>
>
> P.S. My apache configuration is as follows:
>
> I added that to my apache httpd.conf file:
>
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico
> /home/galaxy/galaxy/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt
> [L]
>
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
>
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
>
> I am also attaching my job_conf.xml and galaxy.ini file.
>
>
> ___ 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/
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>
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-04 Thread Makis Ladoukakis
It is uwsgi that I am trying but with apache. Could you let me know what 
changes you made to the configuration of Galaxy?

Thank you,
Makis

Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hi Makis, I recently implemented something like this using uWSGI with a nginx 
frontend. Would you consider using uWSGI instead of your current approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-04 Thread Peter van Heusden
I've written up my experiences in a blog:

http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/

The only Galaxy side changes were the ones mentioned on the Scaling page.
The Bad Gateway message means that Apache can't talk to the uWSGI so what
is the state of uWSGI?

Are you using supervisord? Does supervisorctl show the uWSGI process
running? Does ps ax |grep uwsgi show it running? What does sudo lsof -i
:4001 show is listening on port 4001? That would be the starting point of
my debugging.

Peter
On 4 Dec 2015 10:57, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:

> It is uwsgi that I am trying but with apache. Could you let me know what
> changes you made to the configuration of Galaxy?
>
> Thank you,
> Makis
>
> --
> Date: Fri, 4 Dec 2015 10:01:56 +0200
> Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
> From: p...@sanbi.ac.za
> To: makis4e...@hotmail.com
> CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
>
> Hi Makis, I recently implemented something like this using uWSGI with a
> nginx frontend. Would you consider using uWSGI instead of your current
> approach?
> On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:
>
> Sorry for bumping my own question but I didn't get any replies. Has anyone
> succesfully installed a production Galaxy instance?
>
> I could really use some advice.
>
> Thank you,
> Makis
>
> --
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
>
> Hello everyone,
>
> I am trying to setup a Galaxy instance for a multi-user production
> environment and I tried to follow the instructions here:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh
> --daemon) I got the following error in my browser:Bad Gateway The proxy
> server received an invalid response from an upstream server.
>
>
> I don't get any errors from the paster.log files so I am guessing the
> error is somewhere in my apache configuration although I can't see where it
> could be.
>
>
> Has anyone encountered this problem before?
>
> Kind regards,
> Makis
>
>
> P.S. My apache configuration is as follows:
>
> I added that to my apache httpd.conf file:
>
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico
> /home/galaxy/galaxy/static/favicon.ico [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt
> [L]
>
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
>
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
>
> I am also attaching my job_conf.xml and galaxy.ini file.
>
>
> ___ 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/
>
>
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Please keep all replies on the list by using "reply all"
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-04 Thread Björn Grüning
Hi Makis,

as a small pointer, please have a look at the ansible playrole we provide:

https://github.com/galaxyproject/ansible-galaxy-extras

or the Galaxy Docker Image:

https://github.com/bgruening/docker-galaxy-stable

all steps are described here and can be reused.
Cheers,
Bjoern

Am 04.12.2015 um 08:39 schrieb Makis Ladoukakis:
> Sorry for bumping my own question but I didn't get any replies. Has anyone 
> succesfully installed a production Galaxy instance? 
> 
> I could really use some advice.
> 
> Thank you,
> Makis
> 
> From: makis4e...@hotmail.com
> To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
> Date: Tue, 1 Dec 2015 18:03:44 +0200
> Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed
> 
> 
> 
> 
> Hello everyone,
> 
> I am trying to setup a Galaxy instance for a multi-user production 
> environment and I tried to follow the instructions here:
> 
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
> 
> but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
> --daemon) I got the following error in my browser:Bad Gateway
> The proxy server received an invalid
> response from an upstream server.
> 
> 
> I don't get any errors from the paster.log files so I am guessing the error 
> is somewhere in my apache configuration although I can't see where it could 
> be.
> 
> 
> Has anyone encountered this problem before?
> 
> Kind regards,
> Makis
> 
> 
> P.S. My apache configuration is as follows:
> 
> I added that to my apache httpd.conf file:
> 
> #for galaxy
> #RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
> RewriteRule ^/galaxy$ /galaxy/ [R]
> RewriteRule ^/galaxy/static/style/(.*) 
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
> RewriteRule ^/galaxy/static/scripts/(.*) 
> /home/galaxy/galaxy/static/scripts/packed/$1 [L]
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico 
> [L]
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]
> 
> LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so
> 
> 
> Sethandler uwsgi-handler
> uWSGISocket 127.0.0.1:4001
> uWSGImaxVars 512
> 
> 
> I am also attaching my job_conf.xml and galaxy.ini file.
> 
> 
> 
> ___
> 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/
> 
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-03 Thread Makis Ladoukakis
Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-01 Thread Makis Ladoukakis
Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

galaxy.ini
Description: Binary data


job_conf.xml
Description: XML document
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