Sorry if this is a bad recommendation and if you already tried it and it
doesn't work for Galaxy, but did you know that the MySQL database dump
program mysqldump has a feature to dump the entire database properly for
import into PostgreSQL?
mysqldump --compatible=postgresql [galaxy db name] > galaxy.sql
2011/4/11 Louise-Amélie Schmitt <louise-amelie.schm...@embl.de>
> Hello everyone
> I finally managed to finish my two scripts. It's kind of dirty coded
> (I'm not a Perl fan + I was in a hurry), but at least they worked for
> me. I could successfully transfer the data from an old MySQL Galaxy to
> my new PSQL Galaxy.
> Before running the scripts, you should already have run your new Galaxy
> instance so that the tables are properly created. Please note that the
> scripts will erase everything the target database might contain. It's
> aimed to make a 'clone' of the old database, not to merge both.
> Here is how to do the transfer:
> Requirements: DBD::mysql and DBD:Pg Perl modules
> 1: run galaxy-My2Pg.pl with the appropriate arguments (see the comments
> in the script's first lines)
> 2: start your Galaxy instance
> If the galaxy instance starts without throwing a fit, you can probably
> stop here. (I didn't have that chance though)
> Otherwise you most certainly have the wrong database version:
> 3: run sh manage_db.sh upgrade (to get the version right)
> 4: run galaxy-My2Pg_fix-seq.pl with the appropriate arguments blah, it
> will set the sequences at the right number since manage_db.sh seems to
> mess them up.
> Please note that even if it might work for some other databases, it was
> only tested on Galaxy, and I decline any responsibility if it doesn't
> work, throws data trhough the windows or blows your whole office up. You
> should back your data up beforehand in any case.
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Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at: