from:"Juan Carlos"

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

2015-10-20 Thread Juan Carlos


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  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:
> 
> 
> DirectoryIndex index.html welcome.html
> 
> 
> 
> 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  
> 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

Re: [galaxy-dev] blast2html

2015-10-19 Thread Juan Carlos

HI,
well in case anyone come across a similar problem. I finally found out that
it wasnt a blast specific issue but a general thing. This is I could not
visualize any data, even the one i uploaded, but this didnt happen and
could see everything if i had the module x_accel_redirect disable.
After a while found that this issue was easily solve just adding a "listen
80;" under the nginx configuration.
Now it looks something like this:
server {
client_max_body_size 10G;
listen   80;
server_name  localhost;

#charset koi8-r;

#access_log  logs/host.access.log  main;

...


Didnt check how to solve this issue with the equivalent Apache2 xsendfile.
Just wonder if this should be added to the
https://wiki.galaxyproject.org/Admin/Config/nginxProxy page.


Regards
jc














On Tue, Oct 13, 2015 at 3:01 PM, Juan Carlos <jcsanch...@gmail.com> wrote:

>
>
> Hi all,
> doing some more test realized that when leave "sanitize_all_html = False"
> i cant actually see any html result. So really thinking is something to do
> with the apache2 settings.
> I followed all the step at
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy?action=show=Admin%2FConfig%2FApache+Proxy
> but maybe didnt take into account something else.
> Anyone has any idea to help?
>
> thanks!
> jc
>
>
>
>
> On Fri, Oct 9, 2015 at 12:24 PM, Juan Carlos <jcsanch...@gmail.com> wrote:
>
>> Hi Peter,
>>
>> Just checked it and the HTML output from BLAST+ seems ok.
>> As you said I also think is related to some issue with the security of
>> Galaxy. Everywhere i checked they only mention the sanitize parameter, dont
>> know what else could be, even thinking if it could be something in the
>> apache2 configuration
>> so still trying to find out
>>
>> thanks
>>
>> On Thu, Oct 8, 2015 at 7:04 PM, Peter Cock <p.j.a.c...@googlemail.com>
>> wrote:
>>
>>> Hi Juan,
>>>
>>> It does sounds like something in Galaxy's HTML security
>>> code could be to blame...
>>>
>>> Do you have any other HTML producing tools installed?
>>> It would be useful to see how their output behaves. e.g.
>>> The BLAST+ tools offer (very simple ugly) HTML output
>>> directly.
>>>
>>> Peter
>>>
>>> On Thu, Oct 8, 2015 at 7:54 AM, Juan Carlos <jcsanch...@gmail.com>
>>> wrote:
>>> >
>>> > Hi,
>>> >
>>> > I'm new to galaxy and trying to set up a local blast tool, and maybe
>>> this is
>>> > due to a silly mistake
>>> > So far so good all is working but when trying to use blast2html i just
>>> get a
>>> > "blank" page (even if the html is being generated), this happens when
>>> using
>>> > the recommended setting in the configuration file
>>> > "sanitize_all_html = False"
>>> >
>>> > Tried with "sanitize_all_html = True" and was able to see the results
>>> but
>>> > with the message of the results being stripped.to be sure that at
>>> least
>>> > was working
>>> >
>>> > Thanks for any help!!
>>> > jc
>>> >
>>> > ___
>>> > 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] FW: Galaxy on Centos via Apache - connection refused

2015-10-19 Thread Juan Carlos

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 
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

[galaxy-dev] blast2html

2015-10-08 Thread Juan Carlos

Hi,

I'm new to galaxy and trying to set up a local blast tool, and maybe this
is due to a silly mistake
So far so good all is working but when trying to use blast2html i just get
a "blank" page (even if the html is being generated), this happens when
using the recommended setting in the configuration file
"sanitize_all_html = False"

Tried with "sanitize_all_html = True" and was able to see the results but
with the message of the results being stripped.to be sure that at least
was working

Thanks for any help!!
jc
___
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/

Re: [galaxy-dev] blast2html

2015-10-08 Thread Juan Carlos

Hi Peter,

Just checked it and the HTML output from BLAST+ seems ok.
As you said I also think is related to some issue with the security of
Galaxy. Everywhere i checked they only mention the sanitize parameter, dont
know what else could be, even thinking if it could be something in the
apache2 configuration
so still trying to find out

thanks

On Thu, Oct 8, 2015 at 7:04 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Hi Juan,
>
> It does sounds like something in Galaxy's HTML security
> code could be to blame...
>
> Do you have any other HTML producing tools installed?
> It would be useful to see how their output behaves. e.g.
> The BLAST+ tools offer (very simple ugly) HTML output
> directly.
>
> Peter
>
> On Thu, Oct 8, 2015 at 7:54 AM, Juan Carlos <jcsanch...@gmail.com> wrote:
> >
> > Hi,
> >
> > I'm new to galaxy and trying to set up a local blast tool, and maybe
> this is
> > due to a silly mistake
> > So far so good all is working but when trying to use blast2html i just
> get a
> > "blank" page (even if the html is being generated), this happens when
> using
> > the recommended setting in the configuration file
> > "sanitize_all_html = False"
> >
> > Tried with "sanitize_all_html = True" and was able to see the results but
> > with the message of the results being stripped.to be sure that at
> least
> > was working
> >
> > Thanks for any help!!
> > jc
> >
> > ___
> > 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/

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

Re: [galaxy-dev] blast2html

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

[galaxy-dev] blast2html

Re: [galaxy-dev] blast2html

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