Hi, I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL I've configured apache 2 with this lines on file /etc/apache2/sites-available/default between <VirtualHost> and </VirtualHost> : <Proxy "http://localhost:8080"> Order Deny,Allow Allow from all </Proxy> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/chevalier/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/chevalier/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P] I've configured my MYSQL with a user who have all privilegies on a database and in the universe_wsgi.ini the connection database appears like this : database_connection = mysql://cistrome:cistrome@localhost :/var/run/mysqld/mysqld.sock/cistromeap After running sh run.sh in my galaxy directory, I obtain this error message : .... File "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: ' ' This is the case too when I run this with root privilegies. Is it an error in my configuration of apache 2 or in MySQL ? Or is it an error in my universe_wgsi.ini ? Thank you Julie
On May 16, 2012, at 5:15 AM, julie dubois wrote:
Hi, I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL I've configured apache 2 with this lines on file /etc/apache2/sites-available/default between <VirtualHost> and </VirtualHost> :
<Proxy "http://localhost:8080">
Order Deny,Allow Allow from all </Proxy> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/chevalier/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/chevalier/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P]
I've configured my MYSQL with a user who have all privilegies on a database and in the universe_wsgi.ini the connection database appears like this :
database_connection = mysql://cistrome:cistrome@localhost:/var/run/mysqld/mysqld.sock/cistromeap
After running sh run.sh in my galaxy directory, I obtain this error message : .... File "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: ' '
This is the case too when I run this with root privilegies. Is it an error in my configuration of apache 2 or in MySQL ? Or is it an error in my universe_wgsi.ini ?
Hi Julie, It looks like the 'port =' option in universe.wsgi.ini is uncommented and set to a blank value. Try setting it to 8080 (or comment it back out since 8080 is the default). --nate
Thank you
Julie ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks It was the value of database_connection that was false ! I've changed it by : database_connection=mysql://cistrome:cistrome@localhost :8080/cistromeap?socket=/var/run/mysqld/mysqld.sock It works 2012/5/16 Nate Coraor <nate@bx.psu.edu>
On May 16, 2012, at 5:15 AM, julie dubois wrote:
Hi, I 've installed Galaxy on Ubuntu 12.04 with apache2 and MySQL I've configured apache 2 with this lines on file /etc/apache2/sites-available/default between <VirtualHost> and </VirtualHost> :
<Proxy "http://localhost:8080">
Order Deny,Allow Allow from all </Proxy> RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/chevalier/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/chevalier/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/chevalier/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/chevalier/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/chevalier/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy/(.*) http://localhost:8080$1 [P]
I've configured my MYSQL with a user who have all privilegies on a database and in the universe_wsgi.ini the connection database appears like this :
database_connection = mysql://cistrome:cistrome@localhost :/var/run/mysqld/mysqld.sock/cistromeap
After running sh run.sh in my galaxy directory, I obtain this error message : .... File "/home/chevalier/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/url.py", line 49, in __init__ self.port = int(port) ValueError: invalid literal for int() with base 10: ' '
This is the case too when I run this with root privilegies. Is it an error in my configuration of apache 2 or in MySQL ? Or is it an error in my universe_wgsi.ini ?
Hi Julie,
It looks like the 'port =' option in universe.wsgi.ini is uncommented and set to a blank value. Try setting it to 8080 (or comment it back out since 8080 is the default).
--nate
Thank you
Julie ___________________________________________________________ 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:
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Nate Coraor