Serving a galaxy instance over Apache

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Serving a galaxy instance over Apache

Asma Riyaz
Hi,

I have been through previous issues regarding this issue. So far, I have included the rewrite Engine logic written in /etc/apache2/sites-available/defaults - looks like so:

<VirtualHost *:80>

.....

.....

RewriteEngine on

RewriteRule ^/galaxy$ /galaxy/ [R]

RewriteRule ^/galaxy/static/style/(.*) /seq/SOFTWARE/galaxy/static/june_2007_style/blue/$1 [L]

RewriteRule ^/galaxy/static/scripts/(.*) /seq/SOFTWARE/galaxy/static/scripts/packed/$1 [L]

RewriteRule ^/galaxy/static/(.*) /seq/SOFTWARE/galaxy/static/$1 [L]

RewriteRule ^/galaxy/favicon.ico /seq/SOFTWARE/galaxy/static/favicon.ico [L]

RewriteRule ^/galaxy/robots.txt /seq/SOFTWARE/galaxy/static/robots.txt [L]

RewriteRule ^/galaxy(.*) http://[my IP address]/$1 [P]

I restarted apache after this and accessed : http://[my IP address]/galaxy but no webpage is found. Any advice on how I can proceed to configure the apache correctly?

Thank you,

Asma





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Re: Serving a galaxy instance over Apache

John Chilton-4
This configuration looks correct - are you sure the correct properties
are set in config/galaxy.ini:

You need this section:

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

And [app:main] needs following properties:

filter-with = proxy-prefix
cookie_path = /galaxy

I would also make sure your Galaxy is up and running on port 8080 -
maybe by running a command such as

wget http://127.0.0.1:8080

from the server to make sure you get a response from Galaxy.

If none of that leads to clues - it might be worth starting with the
easier apache proxy configuration (serving on / instead of /galaxy)
and getting that working first to rule out Galaxy and very basic
Apache configuration problems.

-John







On Fri, Apr 17, 2015 at 11:50 AM, Asma Riyaz <[hidden email]> wrote:

> Hi,
>
> I have been through previous issues regarding this issue. So far, I have
> included the rewrite Engine logic written in
> /etc/apache2/sites-available/defaults - looks like so:
>
> <VirtualHost *:80>
>
> .....
>
> .....
>
> RewriteEngine on
>
> RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /seq/SOFTWARE/galaxy/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /seq/SOFTWARE/galaxy/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /seq/SOFTWARE/galaxy/static/$1 [L]
>
> RewriteRule ^/galaxy/favicon.ico /seq/SOFTWARE/galaxy/static/favicon.ico [L]
>
> RewriteRule ^/galaxy/robots.txt /seq/SOFTWARE/galaxy/static/robots.txt [L]
>
> RewriteRule ^/galaxy(.*) http://[my IP address]/$1 [P]
>
> I restarted apache after this and accessed : http://[my IP address]/galaxy
> but no webpage is found. Any advice on how I can proceed to configure the
> apache correctly?
>
> Thank you,
>
> Asma
>
>
>
>
>
> ___________________________________________________________
> 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:
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Re: Serving a galaxy instance over Apache

Asma Riyaz
Hi,

I am setting up apache over a remote server on which a virtual apache was previously installed under /seq/../iwww. Set up of this directory looks something like this:

/seq/../iwww
-->apache/
    -->sites-available/
         -->defaults
    -->sites-enabled/
-->myPublic.conf (this is equivalent to httpd.conf)

As John suggested to start with an easier apache config: 

I have done the following:-
1) In defaults I have this:

<VirtualHost *:80>

.....

.....

RewriteEngine on

RewriteRule ^(.*) [http://[IP address]:8080/]$1 [P]

2) In myPublic.conf I have these two directories:

<Directory "/seq/RNASEQ/iwww/htdocs">

    Options +ExecCGI

    AllowOverride All

    DirectoryIndex index.html index.cgi

    AddHandler cgi-script .cgi

    Order Allow,Deny

    Allow from All

    <FilesMatch "\.ini">

        Deny from all

    </FilesMatch>

</Directory>

<Directory "/seq/regev_genome_portal/SOFTWARE/galaxy">

    AllowOverride All

    DirectoryIndex static/welcome.html

    Order Allow,Deny

    Allow from All

    <FilesMatch "\.ini">

          Deny from all

    </FilesMatch>

At this point I am not sure in which direction should I go to get this running off of apache.

Kindly note: I am able to start an apache instance by executing sh run.sh and the galaxy instance is up and running through the IP address.

Please advice.

Thank you,
Asma



 


On Tue, Apr 21, 2015 at 9:57 AM, John Chilton <[hidden email]> wrote:
This configuration looks correct - are you sure the correct properties
are set in config/galaxy.ini:

You need this section:

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

And [app:main] needs following properties:

filter-with = proxy-prefix
cookie_path = /galaxy

I would also make sure your Galaxy is up and running on port 8080 -
maybe by running a command such as

wget http://127.0.0.1:8080

from the server to make sure you get a response from Galaxy.

If none of that leads to clues - it might be worth starting with the
easier apache proxy configuration (serving on / instead of /galaxy)
and getting that working first to rule out Galaxy and very basic
Apache configuration problems.

-John







On Fri, Apr 17, 2015 at 11:50 AM, Asma Riyaz <[hidden email]> wrote:
> Hi,
>
> I have been through previous issues regarding this issue. So far, I have
> included the rewrite Engine logic written in
> /etc/apache2/sites-available/defaults - looks like so:
>
> <VirtualHost *:80>
>
> .....
>
> .....
>
> RewriteEngine on
>
> RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /seq/SOFTWARE/galaxy/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /seq/SOFTWARE/galaxy/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /seq/SOFTWARE/galaxy/static/$1 [L]
>
> RewriteRule ^/galaxy/favicon.ico /seq/SOFTWARE/galaxy/static/favicon.ico [L]
>
> RewriteRule ^/galaxy/robots.txt /seq/SOFTWARE/galaxy/static/robots.txt [L]
>
> RewriteRule ^/galaxy(.*) http://[my IP address]/$1 [P]
>
> I restarted apache after this and accessed : http://[my IP address]/galaxy
> but no webpage is found. Any advice on how I can proceed to configure the
> apache correctly?
>
> Thank you,
>
> Asma
>
>
>
>
>
> ___________________________________________________________
> 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/