Nothing seems to work on my server. Is Galaxy even compatible with
CentOS? Is there something else that I am missing?
Hello, I'm running a production Galaxy Server on CentOS and I can assure
you it is perfectly feasible. But I'm using NGINX as a web server so I'm
not able to help you with Apache configuration, sorry. Did you try to
use NGINX instead of Apache in order to see if the problem is Apache
related or system related?
Best,
Federico Z.
------------------------------------------------------------------------
From: David.Trudgian(a)UTSouthwestern.edu
To: makis4ever(a)hotmail.com; jcsanchez2(a)gmail.com
CC: galaxy-dev(a)lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +0000
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
refused
SELinux policies are very strict on CentOS by default. Apache isn’t
allowed to access files outside of its standard directories, nor access
network resources. Your local Galaxy apps server is a network resource –
even though it’s local.
If you want to keep SELinux on then use audit2allow to see what policies
will enable access:
cat /var/log/audit/audit.log | audit2allow –v
Then you can use setsebool (temporary) and setsebool –P (permanent) to
enable.
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
*From:*galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org]
*On Behalf Of *Makis Ladoukakis
*Sent:* Friday, October 23, 2015 10:30 AM
*To:* Juan Carlos <jcsanchez2(a)gmail.com>
*Cc:* galaxy-dev(a)lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
refused
Hello,
That didn't work. The apache restart failed with the following error:
SELinux is preventing /usr/sbin/httpd from name_bind access on the
tcp_socket port 8081.
Any idea why?
Kind regards,
Makis
------------------------------------------------------------------------
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
refused
From: jcsanchez2(a)gmail.com <mailto:jcsanchez2@gmail.com>
Date: Tue, 20 Oct 2015 22:25:00 +1030
CC: galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
To: makis4ever(a)hotmail.com <mailto:makis4ever@hotmail.com>
Hi,
If you have a line in your Apache conf like
"Listen 80"
change to
"Listen 8081"
On 20 Oct 2015, at 21:00, Makis Ladoukakis <makis4ever(a)hotmail.com
<mailto:makis4ever@hotmail.com>> wrote:
Hello,
I am sorry but I have really no experience with setting up the
Apache web server so I am not really sure how to do that. Can you
please help me out with it? My apache configuration file is in
/etc/httpd/conf/ directory and there are no directories such as
/sites-available/ or /sites-enabled/ (as I would find in an ubuntu
installation).
What I did already (after some advice from the server admin) is open
up the 8081 port like that:
firewall-cmd --permanent --add-port=8081/tcp
firewall-cmd --reload
and then I got another error:
[cgi:error] [pid 29603] [client 115.230.124.164:4559] script not
found or unable to stat: /var/www/cgi-bin/common
[autoindex:error] [pid 29716] [client 218.76.28.36:4468] AH01276:
Cannot serve directory /var/www/html/: No matching DirectoryIndex
(index.html,index.php) found, and server-generated directory index
forbidden by Options directive
which I tried to solve by adding welcome.html as a recognizable
filename in the apache configuration:
<IfModule dir_module>
DirectoryIndex index.html welcome.html
</IfModule>
but nothing worked and now the error_log shows the following:
[Tue Oct 20 13:15:23.719295 2015] [mpm_prefork:notice] [pid 29598]
AH00170: caught SIGWINCH, shutting down gracefully
[Tue Oct 20 13:15:24.810684 2015] [core:notice] [pid 46896] SELinux
policy enabled; httpd running as context system_u:system_r:httpd_t:s0
[Tue Oct 20 13:15:24.811647 2015] [suexec:notice] [pid 46896]
AH01232: suEXEC mechanism enabled (wrapper: /usr/sbin/suexec)
[Tue Oct 20 13:15:24.846399 2015] [so:warn] [pid 46896] AH01574:
module wsgi_module is already loaded, skipping
[Tue Oct 20 13:15:24.847316 2015] [auth_digest:notice] [pid 46896]
AH01757: generating secret for digest authentication ...
[Tue Oct 20 13:15:24.848294 2015] [lbmethod_heartbeat:notice] [pid
46896] AH02282: No slotmem from mod_heartmonitor
[Tue Oct 20 13:15:24.870033 2015] [mpm_prefork:notice] [pid 46896]
AH00163: Apache/2.4.6 (CentOS) PHP/5.4.16 mod_wsgi/3.4 Python/2.7.5
configured -- resuming normal operations
[Tue Oct 20 13:15:24.870075 2015] [core:notice] [pid 46896] AH00094:
Command line: '/usr/sbin/httpd -D FOREGROUND'
And the webpage that galaxy is supposed to appear is still blank.
Any ideas?
Thank you,
Makis
------------------------------------------------------------------------
Date: Tue, 20 Oct 2015 11:01:44 +1030
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache -
connection refused
From: jcsanchez2(a)gmail.com <mailto:jcsanchez2@gmail.com>
To: makis4ever(a)hotmail.com <mailto:makis4ever@hotmail.com>
CC: galaxy-dev(a)lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
hi,
Maybe sounds silly, but have you tried to put the apache
configuration in a virtual host within the sites-enable site?
cheers
jc
On Tue, Oct 20, 2015 at 12:36 AM, Makis Ladoukakis
<makis4ever(a)hotmail.com <mailto:makis4ever@hotmail.com>> wrote:
Forwading to this list too. I am not sure if they are two
separate lists.
Makis
------------------------------------------------------------------------
From: makis4ever(a)hotmail.com <mailto:makis4ever@hotmail.com>
To: galaxy-dev(a)lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>
Date: Mon, 19 Oct 2015 17:04:13 +0300
Subject: [galaxy-dev] Galaxy on Centos via Apache - connection
refused
Dear all,
I've been trying to set up a Galaxy instance on my CentOS server
but even when I manage to run the simplest configuration
correctly I can't seem to get it right on my browser as the
connection is refused.
I have changed the host to 0.0.0.0, the port to 8081 and made
the appropriate changes in Apache configuration file:
RewriteEngine on
RewriteRule ^/galaxy_test(.*)
http://localhost:8081$1 [P]
RewriteRule ^/galaxy_test$ /galaxy_test/ [R]
RewriteRule ^/galaxy_test/static/style/(.*)
/home/galaxy_test/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy_test/static/scripts/(.*)
/home/galaxy_test/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy_test/static/(.*)
/home/galaxy_test/galaxy/static/$1 [L]
RewriteRule ^/galaxy_test/favicon.ico
/home/galaxy_test/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy_test/robots.txt
/home/galaxy_test/galaxy/static/robots.txt [L]
So when I tried to run it the first time I got the "temporarily
out of service" error on my browser and the following error in
apache log:
[Mon Oct 19 05:56:45.308714 2015] [proxy:error] [pid 18505]
(13)Permission denied: AH00957: HTTP: attempt to connect to
127.0.0.1:8081 <
http://127.0.0.1:8081> (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505]
[client 185.25.151.159:39629 <
http://185.25.151.159:39629>]
AH01114: HTTP: failed to make connection to backend: localhost
Searching the internet I found the following solution:
/usr/sbin/setsebool httpd_can_network_connect 1
/usr/sbin/setsebool -P httpd_can_network_connect 1
but when I restarted my galaxy my browser would now show just a
blank page and the error log of apache was:
[Mon Oct 19 15:29:09.425120 2015] [proxy:error] [pid 29699]
(111)Connection refused: AH00957: HTTP: attempt to connect to
127.0.0.1:8081 <
http://127.0.0.1:8081> (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699]
[client 147.102.86.121:51865 <
http://147.102.86.121:51865>]
AH01114: HTTP: failed to make connection to backend: localhost
Has anyone encountered that?
Kind regards,
Makis
P.S. In case that helps the output of iptables -L is the following:
Chain INPUT (policy ACCEPT)
target prot opt source destination
ACCEPT all -- anywhere anywhere
ctstate RELATED,ESTABLISHED
ACCEPT all -- anywhere anywhere
INPUT_direct all -- anywhere anywhere
INPUT_ZONES_SOURCE all -- anywhere anywhere
INPUT_ZONES all -- anywhere anywhere
ACCEPT icmp -- anywhere anywhere
REJECT all -- anywhere anywhere
reject-with icmp-host-prohibited
Chain FORWARD (policy ACCEPT)
target prot opt source destination
ACCEPT all -- anywhere anywhere
ctstate RELATED,ESTABLISHED
ACCEPT all -- anywhere anywhere
FORWARD_direct all -- anywhere anywhere
FORWARD_IN_ZONES_SOURCE all -- anywhere anywhere
FORWARD_IN_ZONES all -- anywhere anywhere
FORWARD_OUT_ZONES_SOURCE all -- anywhere anywhere
FORWARD_OUT_ZONES all -- anywhere anywhere
ACCEPT icmp -- anywhere anywhere
REJECT all -- anywhere anywhere
reject-with icmp-host-prohibited
Chain OUTPUT (policy ACCEPT)
target prot opt source destination
OUTPUT_direct all -- anywhere anywhere
Chain FORWARD_IN_ZONES (1 references)
target prot opt source destination
FWDI_public all -- anywhere anywhere
[goto]
FWDI_public all -- anywhere anywhere
[goto]
Chain FORWARD_IN_ZONES_SOURCE (1 references)
target prot opt source destination
Chain FORWARD_OUT_ZONES (1 references)
target prot opt source destination
FWDO_public all -- anywhere anywhere
[goto]
FWDO_public all -- anywhere anywhere
[goto]
Chain FORWARD_OUT_ZONES_SOURCE (1 references)
target prot opt source destination
Chain FORWARD_direct (1 references)
target prot opt source destination
Chain FWDI_public (2 references)
target prot opt source destination
FWDI_public_log all -- anywhere anywhere
FWDI_public_deny all -- anywhere anywhere
FWDI_public_allow all -- anywhere anywhere
Chain FWDI_public_allow (1 references)
target prot opt source destination
Chain FWDI_public_deny (1 references)
target prot opt source destination
Chain FWDI_public_log (1 references)
target prot opt source destination
Chain FWDO_public (2 references)
target prot opt source destination
FWDO_public_log all -- anywhere anywhere
FWDO_public_deny all -- anywhere anywhere
FWDO_public_allow all -- anywhere anywhere
Chain FWDO_public_allow (1 references)
target prot opt source destination
Chain FWDO_public_deny (1 references)
target prot opt source destination
Chain FWDO_public_log (1 references)
target prot opt source destination
Chain INPUT_ZONES (1 references)
target prot opt source destination
IN_public all -- anywhere anywhere [goto]
IN_public all -- anywhere anywhere [goto]
Chain INPUT_ZONES_SOURCE (1 references)
target prot opt source destination
Chain INPUT_direct (1 references)
target prot opt source destination
Chain IN_public (2 references)
target prot opt source destination
IN_public_log all -- anywhere anywhere
IN_public_deny all -- anywhere anywhere
IN_public_allow all -- anywhere anywhere
Chain IN_public_allow (1 references)
target prot opt source destination
ACCEPT tcp -- anywhere anywhere
tcp dpt:http ctstate NEW
ACCEPT tcp -- anywhere anywhere
tcp dpt:ssh ctstate NEW
ACCEPT tcp -- anywhere anywhere
tcp dpt:https ctstate NEW
Chain IN_public_deny (1 references)
target prot opt source destination
Chain IN_public_log (1 references)
target prot opt source destination
Chain OUTPUT_direct (1 references)
target prot opt source destination
___________________________________________________________
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Galaxy lists, please use the interface at:
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___________________________________________________________
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/
------------------------------------------------------------------------
UTSouthwestern
Medical Center
The future of medicine, today.
___________________________________________________________
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/