Greg,
please see in-line:
2009/7/23 Greg Von Kuster ghv2@psu.edu
Hi Erick,
Erick Antezana wrote:
Greg,
I manage to set my connection string so that we could use a remote mysql server. Thanks.
w.r.t. the datasets purging, I used the scripts to clean deleted libraries, folders, datasets, userless history ... I've seen that one must speficy the span of time in days. What about the data that was added mistakenly for instance today and that we want to immediately delete it? I tried to launch the script with "-d 0" but the data is still there... Am I missing something?
No, I don't think so. It's possible that your system clock is off from your database time.
both servers (mysql and the one where galaxy is running) have the same time.
Is your database storing time as local time?
how can I see that?
The cleanup script uses the update_time for the objects being deleted.
In which file can I find the SQL command that actually deletes and purges the data?
I am no longer using the sqlite DB created in our first trials. I guess I can safely delete (from the command line) all the files under the directory database?
Maybe. Did you keep any data that refers to them in your tables when you migrated to mysql? If so, you'll need to keep them.
no, I have no data referring to anything... I just deleted (to save space) all those files and I have no problems at all (so far ;-) )
have the purge_*.sh scripts tested with mysql?
Yes
last question (already asked before): are there any plans to support Oracle?
Not sure why it wouldn't already be supported, although we don't use it here. Just needs a different URL - sqlalchemy supports Oracle.
good to know that, I will try to find some time to test it and let you know.
cheers, Erick
thanks, Erick
2009/7/22 Greg Von Kuster <ghv2@psu.edu mailto:ghv2@psu.edu>
Erick,
To use a different database than the sqlite that come with the Galaxy distribution all that is needed is to change the config setting, prviding the URL that points to your mysql database. See the mysql documentation for the connection URL, as the URL differs depending upon whether you database is installed locally or not.
The config setting is the "database_connection" setting, and could look something like this:
database_connection = mysql:///greg_test?unix_socket=/var/run/mysqld/mysqld.sock
Greg Von Kuster Galaxy Development Team
Erick Antezana wrote:
Hello, I would like to use MySQL instead of sqlite to store my data. I coudn't find on the Galaxy web site a HOWTO or some guidelines to do it. I only found some lines that might need to be changed/enabled in the universe_wsgi.ini file: #database_file = database/universe.sqlite database_connection = mysql:///galaxy #database_engine_option_echo = true #database_engine_option_echo_pool = true #database_engine_option_pool_size = 10 #database_engine_option_max_overflow = 20 Could you point out to some doc or briefly describe what I need to do in order to go for mysql? Are there any plans to support other DBMS's (like Oracle for instance)? thanks, Erick
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