Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

Nothing seems to work on my server. Is Galaxy even compatible with CentOS? Is there something else that I am missing?

------------------------------------------------------------------------ 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&gt; *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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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