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
> 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 and
> :
> >
> > http://localhost:8080";>
> >
> > Order Deny,Allow
> > Allow from all
> >
> > 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
> > ___
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>
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