Apache configuration for galaxy - currently routing display_application requests to root.

apache.log

## Starting up Local IGV, which grabs the list of genomes (genomes.txt)
x.x.x.x - - [22/Jun/2012:14:31:39 +0800] "GET /igv/genomes.txt HTTP/1.1" 200 8035 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:31:39 +0800] "HEAD /igv/sn15.genome HTTP/1.1" 200 273 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"

## Clicking the Local "Display with IGV" link from inside Galaxy
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default HTTP/1.1" 302 855 "http://example.org/galaxy/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam.bai HTTP/1.1" 302 1251 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "GET /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam.bai&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 28036 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "HEAD /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam HTTP/1.1" 302 568 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "HEAD /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 391 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:32:38 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam HTTP/1.1" 302 1238 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:32:39 +0800] "GET /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 28036 "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"

default

<VirtualHost *:80>
	ServerAdmin webmaster@localhost

	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>

	<Directory /var/www/w>
		AllowOverride All
	</Directory>

	ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
	<Directory "/usr/lib/cgi-bin">
		AllowOverride None
		Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
		Order allow,deny
		Allow from all
	</Directory>

	ErrorLog ${APACHE_LOG_DIR}/error.log

	# Possible values include: debug, info, notice, warn, error, crit,
	# alert, emerg.
	LogLevel warn

	CustomLog ${APACHE_LOG_DIR}/access.log combined

	Alias /doc/ "/usr/share/doc/"
	<Directory "/usr/share/doc/">
		Options Indexes MultiViews FollowSymLinks
		AllowOverride None
		Order deny,allow
		Deny from all
		Allow from 127.0.0.0/255.0.0.0 ::1/128
	</Directory>
	
	RewriteEngine on
	RewriteRule ^/galaxy$ /galaxy/ [R]
	RewriteRule ^/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
	RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
	RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
	RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
	RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
	RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
	
	
	Alias /wiki /var/www/w/index.php
        <Location "/galaxy">
                XSendFile on
                XSendFilePath /
        </Location>

        <LocationMatch display_application/[a-zA-Z0-9]+/igv.*>
                RequestHeader set REMOTE_USER igv_display@example.org
                Satisfy Any
                Order deny,allow
                Allow from all
        </LocationMatch>
</VirtualHost>

Galaxy.stderr

## Clicking the Local "Display with IGV" link from inside Galaxy
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default HTTP/1.1" 302 - "http://example.org/galaxy/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam.bai HTTP/1.1" 302 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
galaxy.web.framework DEBUG 2012-06-22 14:42:40,176 Error: this request returned None from get_history(): http://example.org/galaxy/root
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "GET /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam.bai&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "HEAD /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam HTTP/1.1" 302 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
galaxy.web.framework DEBUG 2012-06-22 14:42:40,238 Error: this request returned None from get_history(): http://example.org/galaxy/root
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "HEAD /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "GET /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam HTTP/1.1" 302 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"
galaxy.web.framework DEBUG 2012-06-22 14:42:40,313 Error: this request returned None from get_history(): http://example.org/galaxy/root
x.x.x.x - - [22/Jun/2012:14:42:40 +0800] "GET /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf HTTP/1.1" 200 - "-" "IGV Version 2.1.18 (2530)06/10/2012 09:58 PM"