Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
I am not very good with Apache rewrite rules, but I think there is a problem with (at least) the first rule. I see in the Apache documentation [1] that the following “doesn’t make sense, not supported": ^/somepath(.*) http://thishost/otherpath$1 [P] The [P] flag is for forwarding to a proxy, but you are forwarding to localhost (i.e. http://thishost) not a proxy. So try changing the first rule to RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 That is, remove the [P] from the end, and see if that makes a difference. The other rules look ok, although so did the above at first glance, so you might want to add one rules at a time to help you isolate rules that are causing problems. Hope that helps, Keith 1. http://httpd.apache.org/docs/current/mod/mod_rewrite.html > On Nov 4, 2015, at 6:08 AM, Makis Ladoukakis <makis4e...@hotmail.com> wrote: > > So yeah you might be on to something here. When I commented the Rewrite rules > I could access my galaxy instance from myservername:8081 with or without the > index.html file placed in /var/www/html. When I did place it in the directory > though and I tried with the rewrite rules my server gave me the following > error: > > script not found or unable to stat: /var/www/cgi-bin/common > > and once again the galaxy page was blank. > > Any ideas why? What is apache's problem with the rewrite rules being there? > > thank you, > Makis > > Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused > From: suder...@cs.vassar.edu > Date: Tue, 3 Nov 2015 13:06:03 -0500 > CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org > To: makis4e...@hotmail.com > > Very odd that you were getting "Address is use" errors then.. What have you > set the port to in your galaxy.ini file? > > The missing index.html/index.php won't make a difference to Galaxy, but it > might prevent Apache from starting up. I would put a simple index.html file, > say: > > You should not see this. > > in /var/www/html just so Apache is happy and if you see that at least you > will know Apache is up and running and listening on the correct ports. I > would also forego the Apache rewrite rules until you know Galaxy is working. > > Keith > > On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis <makis4e...@hotmail.com > <mailto:makis4e...@hotmail.com>> wrote: > > Νο, no other service is running on 8081. This is the output of netstat -tulpn: > > tcp0 0 0.0.0.0:33060.0.0.0:* LISTEN > - > tcp0 0 0.0.0.0:22 0.0.0.0:* LISTEN > - > tcp0 0 127.0.0.1:250.0.0.0:* LISTEN > - > tcp6 0 0 :::80 :::*LISTEN > - > tcp6 0 0 :::22 :::*LISTEN > - > tcp6 0 0 ::1:25 :::*LISTEN > - > udp0 0 0.0.0.0:123 0.0.0.0:* > - > udp0 0 127.0.0.1:323 0.0.0.0:* > - > udp0 0 0.0.0.0:53530.0.0.0:* > - > udp0 0 0.0.0.0:33715 0.0.0.0:* > - > udp6 0 0 :::123 :::* > - > udp6 0 0 ::1:323 :::* > > And no I only have an info.php in that directory. Does that affect Galaxy in > any way? > > Thank you, > Makis > > Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused > From: suder...@cs.vassar.edu <mailto:suder...@cs.vassar.edu> > Date: Tue, 3 Nov 2015 12:07:12 -0500 > CC: federico.zambe...@gmail.com <mailto:federico.zambe...@gmail.com>; > galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com> > > Do you have another service running on 8081? I see the server is complaining > about that address already being in use. Also, do you have an index.html or > welcome.html in /var/www/html? > > Cheers, > Keith > > On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis <makis4e...@hotmail.com > <mailto:makis4e...@hotmail.com>> wrote: > > Hello, > > Unfortunately I cannot change web servers at the moment. There are a lot of > applications that I would need to make changes for the nginx configuration > plus i am not very experienced with nginx (apparently not with apache as well > outside debian systems). > > Thank you, >
Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
So yeah you might be on to something here. When I commented the Rewrite rules I could access my galaxy instance from myservername:8081 with or without the index.html file placed in /var/www/html. When I did place it in the directory though and I tried with the rewrite rules my server gave me the following error: script not found or unable to stat: /var/www/cgi-bin/common and once again the galaxy page was blank. Any ideas why? What is apache's problem with the rewrite rules being there? thank you, Makis Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused From: suder...@cs.vassar.edu Date: Tue, 3 Nov 2015 13:06:03 -0500 CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org To: makis4e...@hotmail.com Very odd that you were getting "Address is use" errors then.. What have you set the port to in your galaxy.ini file? The missing index.html/index.php won't make a difference to Galaxy, but it might prevent Apache from starting up. I would put a simple index.html file, say: You should not see this. in /var/www/html just so Apache is happy and if you see that at least you will know Apache is up and running and listening on the correct ports. I would also forego the Apache rewrite rules until you know Galaxy is working. Keith On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis <makis4e...@hotmail.com> wrote:Νο, no other service is running on 8081. This is the output of netstat -tulpn: tcp0 0 0.0.0.0:33060.0.0.0:* LISTEN - tcp0 0 0.0.0.0:22 0.0.0.0:* LISTEN - tcp0 0 127.0.0.1:250.0.0.0:* LISTEN - tcp6 0 0 :::80 :::*LISTEN - tcp6 0 0 :::22 :::*LISTEN - tcp6 0 0 ::1:25 :::*LISTEN - udp0 0 0.0.0.0:123 0.0.0.0:* - udp0 0 127.0.0.1:323 0.0.0.0:* - udp0 0 0.0.0.0:53530.0.0.0:* - udp0 0 0.0.0.0:33715 0.0.0.0:* - udp6 0 0 :::123 :::* - udp6 0 0 ::1:323 :::* And no I only have an info.php in that directory. Does that affect Galaxy in any way? Thank you, Makis Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused From: suder...@cs.vassar.edu Date: Tue, 3 Nov 2015 12:07:12 -0500 CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org To: makis4e...@hotmail.com Do you have another service running on 8081? I see the server is complaining about that address already being in use. Also, do you have an index.html or welcome.html in /var/www/html? Cheers,Keith On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis <makis4e...@hotmail.com> wrote:Hello, Unfortunately I cannot change web servers at the moment. There are a lot of applications that I would need to make changes for the nginx configuration plus i am not very experienced with nginx (apparently not with apache as well outside debian systems). Thank you, Makis > To: galaxy-dev@lists.galaxyproject.org > From: federico.zambe...@gmail.com > Date: Tue, 3 Nov 2015 17:19:59 +0100 > Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection > refused > > Il 03/11/15 11:53, Makis Ladoukakis ha scritto: > > > > > 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.trudg...@utsouthwestern.edu > > To: makis4e...@hotmail.com; jcsanch...@gmail.com > > CC: galaxy-...@lists.bx.psu.edu > > Date: Fri, 23 Oct 2015 17:30:51 + > > 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: >
Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
Very odd that you were getting “Address is use” errors then.. What have you set the port to in your galaxy.ini file? The missing index.html/index.php won’t make a difference to Galaxy, but it might prevent Apache from starting up. I would put a simple index.html file, say: You should not see this. in /var/www/html just so Apache is happy and if you see that at least you will know Apache is up and running and listening on the correct ports. I would also forego the Apache rewrite rules until you know Galaxy is working. Keith > On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis <makis4e...@hotmail.com> wrote: > > Νο, no other service is running on 8081. This is the output of netstat -tulpn: > > tcp0 0 0.0.0.0:33060.0.0.0:* LISTEN > - > tcp0 0 0.0.0.0:22 0.0.0.0:* LISTEN > - > tcp0 0 127.0.0.1:250.0.0.0:* LISTEN > - > tcp6 0 0 :::80 :::*LISTEN > - > tcp6 0 0 :::22 :::*LISTEN > - > tcp6 0 0 ::1:25 :::*LISTEN > - > udp0 0 0.0.0.0:123 0.0.0.0:* > - > udp0 0 127.0.0.1:323 0.0.0.0:* > - > udp0 0 0.0.0.0:53530.0.0.0:* > - > udp0 0 0.0.0.0:33715 0.0.0.0:* > - > udp6 0 0 :::123 :::* > - > udp6 0 0 ::1:323 :::* > > And no I only have an info.php in that directory. Does that affect Galaxy in > any way? > > Thank you, > Makis > > Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused > From: suder...@cs.vassar.edu <mailto:suder...@cs.vassar.edu> > Date: Tue, 3 Nov 2015 12:07:12 -0500 > CC: federico.zambe...@gmail.com <mailto:federico.zambe...@gmail.com>; > galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com> > > Do you have another service running on 8081? I see the server is complaining > about that address already being in use. Also, do you have an index.html or > welcome.html in /var/www/html? > > Cheers, > Keith > > On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis <makis4e...@hotmail.com > <mailto:makis4e...@hotmail.com>> wrote: > > Hello, > > Unfortunately I cannot change web servers at the moment. There are a lot of > applications that I would need to make changes for the nginx configuration > plus i am not very experienced with nginx (apparently not with apache as well > outside debian systems). > > Thank you, > Makis > > > To: galaxy-dev@lists.galaxyproject.org > > <mailto:galaxy-dev@lists.galaxyproject.org> > > From: federico.zambe...@gmail.com <mailto:federico.zambe...@gmail.com> > > Date: Tue, 3 Nov 2015 17:19:59 +0100 > > Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection > > refused > > > > Il 03/11/15 11:53, Makis Ladoukakis ha scritto: > > > > > > > > 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.trudg...@utsouthwestern.edu > > > <mailto:david.trudg...@utsouthwestern.edu> > > > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com>; > > > jcsanch...@gmail.com <mailto:jcsanch...@gmail.com> > > > CC: galaxy-...@lists.bx.psu.edu <mailto:galaxy-...@lists.bx.psu.edu> > > > Date: Fri, 23 Oct 2015 17:30:51 + > > > 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 &g
