So I disabled SELinux
But that didn't make any difference. While the run.sh runs I still can't see
anything but a blank page.
When I changed my apache configuration to include port 8081, the script didn't
even run producing the error:
Traceback (most recent call last):
File "./scripts/paster.py", line 32, in <module>
serve.run()
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line
1052, in run
invoke(command, command_name, options, args[1:])
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line
1058, in invoke
exit_code = runner.run(args)
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line
221, in run
result = self.command()
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line
664, in command
serve()
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line
648, in serve
server(app)
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
294, in server_wrapper
**context.local_conf)
File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line
99, in fix_call
val = callable(*args, **kw)
File
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1342, in server_runner
serve(wsgi_app, **kwargs)
File
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1291, in serve
request_queue_size=request_queue_size)
File
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1134, in __init__
request_queue_size=request_queue_size)
File
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1113, in __init__
request_queue_size=request_queue_size)
File
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
File "/usr/lib64/python2.7/SocketServer.py", line 419, in __init__
self.server_bind()
File "/usr/lib64/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
File "/usr/lib64/python2.7/SocketServer.py", line 430, in server_bind
self.socket.bind(self.server_address)
File "/usr/lib64/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 98] Address already in use
That error was the same when I changed 80 to 8081 and when I added a second
Listen with 8081.
Nothing seems to work on my server. Is Galaxy even compatible with CentOS? Is
there something else that I am missing?
Any help would be appreciated. This installation seems impossible.
Thank you,
Makis
From: david.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@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-boun...@lists.galaxyproject.org]
On Behalf Of Makis Ladoukakis
Sent: Friday, October 23, 2015 10:30 AM
To: Juan Carlos <jcsanch...@gmail.com>
Cc: galaxy-...@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: jcsanch...@gmail.com
Date: Tue, 20 Oct 2015 22:25:00 +1030
CC: galaxy-...@lists.bx.psu.edu
To: makis4e...@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 <makis4e...@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: jcsanch...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@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 <makis4e...@hotmail.com>
wrote:
Forwading to this list too. I am not sure if they are two separate lists.
Makis
From:
makis4e...@hotmail.com
To: 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 (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505] [client
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 (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699] [client
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
___________________________________________________________ Please keep all
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subscriptions to this and other Galaxy
lists, please use the interface at:
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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/
UT
Southwestern
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/
