Hi Louise,

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

regards,
Leandro

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.
>
> Cheers,
> LA
>
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