Hi Neil,

with your current apache configuration, you should probably see Galaxy at http://yourip/galaxy This is due to your Rewriterule /galaxy and for that you have also set proxy_prefix = /galaxy in your universe_wsgi.ini

You should probably remove the empty galaxy directory under /var/www Furthermore, most of the time you will not need a directory with 777 in your apache web/documentroot..

Cheers, Jelle

On Thu, Aug 23, 2012 at 8:34 AM, Neil.Burdett@csiro.au wrote:

Hi I've installed galaxy with the default settings and it works fine.

On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation.

After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html

Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add ":8080" after the ip address. Is this still required? I thought that Apache would know to redirect to my distribution....What am I doing wrong?

/etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ...

    DocumentRoot /var/www
    <Directory />
            Options FollowSymLinks
            AllowOverride None
    </Directory>
    <Directory /var/www/>
            Options Indexes FollowSymLinks MultiViews
            AllowOverride None
            Order allow,deny
            allow from all
    </Directory>

etc ...

/var/www/.htaccess

RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

I created an empty 'galaxy' directory with 777 permissions on it under /var/www

and universe_wsgi.ini

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

# ---- Galaxy ---------------------------------------------------------------

# Configuration of the Galaxy application.

[app:main] filter-with = proxy-prefix cookie_path = /galaxy

Thanks Neil

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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Hi Neil,

I'm certainly not an apache expert so I might be giving you the wrong advise, but try adding the following: LoadModule proxy_module modules/mod_proxy.so LoadModule proxy_http_module modules/mod_proxy_http.so

If above fails, try to go back to the simplest configuration mentioned on the galaxy wiki: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Thus: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P]

Which would make your galaxy instance available on http://yourip

From there you can further debug if it doesn't work :)

Cheers, Jelle

On Thu, Aug 23, 2012 at 11:48 PM, Neil.Burdett@csiro.au wrote:

Hi Jelle, I'm still having issues with Apache. I've moved

RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

from /var/www/.htaccess to /etc/apache2/httpd.conf

I still get a "404 Not found" error when trying to access galaxy (http://140.253.78.44/galaxy )

http://140.253.78.44 still gets the "It Works!" Apache default index.html

and http://140.253.78.44:8080 gets the galaxy page

/var/log/apache2/error.log states...

[Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does not exist: /var/www/favicon.ico [Fri Aug 24 07:36:25 2012] [error] [client 140.253.78.44] File does not exist: /var/www/galaxy

Now if I change httpd.conf and add the vitrtualHost tags to:

ServerName localhost <VirtualHost *:80> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

</VirtualHost>

I now get a "403 Forbidden" error when trying to access (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ on this server, and /var/log/apache2/error.log states..

[Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to make remote request from mod_rewrite without proxy enabled: proxy:http://localhost:8080/ [Fri Aug 24 07:45:34 2012] [error] [client 140.253.78.44] File does not exist: /etc/apache2/htdocs

Any help much appreciated

Neil ________________________________________ From: Jelle Scholtalbers [j.scholtalbers@gmail.com] Sent: Thursday, August 23, 2012 8:20 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Installing galaxy with Apache ...

Hi Neil,

with your current apache configuration, you should probably see Galaxy at http://yourip/galaxy This is due to your Rewriterule /galaxy and for that you have also set proxy_prefix = /galaxy in your universe_wsgi.ini

You should probably remove the empty galaxy directory under /var/www Furthermore, most of the time you will not need a directory with 777 in your apache web/documentroot..

Cheers, Jelle

On Thu, Aug 23, 2012 at 8:34 AM, Neil.Burdett@csiro.au wrote:

...

Hi I've installed galaxy with the default settings and it works fine.

On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation.

After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html

Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add ":8080" after the ip address. Is this still required? I thought that Apache would know to redirect to my distribution....What am I doing wrong?

/etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ...

    DocumentRoot /var/www
    <Directory />
            Options FollowSymLinks
            AllowOverride None
    </Directory>
    <Directory /var/www/>
            Options Indexes FollowSymLinks MultiViews
            AllowOverride None
            Order allow,deny
            allow from all
    </Directory>

etc ...

/var/www/.htaccess

RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

I created an empty 'galaxy' directory with 777 permissions on it under /var/www

and universe_wsgi.ini

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

# ---- Galaxy ---------------------------------------------------------------

# Configuration of the Galaxy application.

[app:main] filter-with = proxy-prefix cookie_path = /galaxy

Thanks Neil

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

Thanks very much. This did in fact solve the issue. For those following the thread the "Rewrite" statements have to be added to /etc/apache2/sites-available/defaults.

Thanks Again Neil

-----Original Message----- From: Carlos Borroto [mailto:carlos.borroto@gmail.com] Sent: Tuesday, 28 August 2012 6:14 AM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Installing galaxy with Apache ...

This thread my help you: http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.ht...

On Thu, Aug 23, 2012 at 5:48 PM, Neil.Burdett@csiro.au wrote:

Hi Jelle, I'm still having issues with Apache. I've moved

RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

from /var/www/.htaccess to /etc/apache2/httpd.conf

I still get a "404 Not found" error when trying to access galaxy (http://140.253.78.44/galaxy )

http://140.253.78.44 still gets the "It Works!" Apache default index.html

and http://140.253.78.44:8080 gets the galaxy page

/var/log/apache2/error.log states...

[Fri Aug 24 07:35:27 2012] [error] [client 140.253.78.44] File does not exist: /var/www/favicon.ico [Fri Aug 24 07:36:25 2012] [error] [client 140.253.78.44] File does not exist: /var/www/galaxy

Now if I change httpd.conf and add the vitrtualHost tags to:

ServerName localhost <VirtualHost *:80> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] </VirtualHost>

I now get a "403 Forbidden" error when trying to access (http://140.253.78.44/galaxy ) You don't have permission to access /galaxy/ on this server, and /var/log/apache2/error.log states..

[Fri Aug 24 07:45:33 2012] [error] [client 140.253.78.44] attempt to make remote request from mod_rewrite without proxy enabled: proxy:http://localhost:8080/ [Fri Aug 24 07:45:34 2012] [error] [client 140.253.78.44] File does not exist: /etc/apache2/htdocs

Any help much appreciated

Neil ________________________________________ From: Jelle Scholtalbers [j.scholtalbers@gmail.com] Sent: Thursday, August 23, 2012 8:20 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Installing galaxy with Apache ...

Hi Neil,

with your current apache configuration, you should probably see Galaxy at http://yourip/galaxy This is due to your Rewriterule /galaxy and for that you have also set proxy_prefix = /galaxy in your universe_wsgi.ini

You should probably remove the empty galaxy directory under /var/www Furthermore, most of the time you will not need a directory with 777 in your apache web/documentroot..

Cheers, Jelle

On Thu, Aug 23, 2012 at 8:34 AM, Neil.Burdett@csiro.au wrote:

...

Hi I've installed galaxy with the default settings and it works fine.

On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation.

After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html

Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add ":8080" after the ip address. Is this still required? I thought that Apache would know to redirect to my distribution....What am I doing wrong?

/etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ...

    DocumentRoot /var/www
    <Directory />
            Options FollowSymLinks
            AllowOverride None
    </Directory>
    <Directory /var/www/>
            Options Indexes FollowSymLinks MultiViews
            AllowOverride None
            Order allow,deny
            allow from all
    </Directory>

etc ...

/var/www/.htaccess

RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

I created an empty 'galaxy' directory with 777 permissions on it under /var/www

and universe_wsgi.ini

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

# ---- Galaxy

# Configuration of the Galaxy application.

[app:main] filter-with = proxy-prefix cookie_path = /galaxy

Thanks Neil

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/