Question: Save and load complete histories
gravatar for Philipp.rathert
2.0 years ago by
Philipp.rathert30 wrote:

dear all,

i am running a local galaxy instance but have some problems with it (difficult to explain). However, I want to kill the complete instance and reinstall. Therefore I want to save all old histories and export them as data file. I get a xy.tar.gz file on my computer but when I want to import the history again via "import from file" I just get the option to import from an "Archived history URL". When I paste the file location in nothing happens...

what am I missing?

Do I need to upload in a different way?

Thanks a lot for your help...

histories • 571 views
ADD COMMENTlink written 2.0 years ago by Philipp.rathert30

Hi Philip

Not answer, just another suggestion: How about copying your old <galaxy-root>/database/files/ directory to your new instance and connect your new instance to the old PostgreSQL DB (assuming the the two instances are running the same DB version)?


ADD REPLYlink written 2.0 years ago by Hotz, Hans-Rudolf1.7k

Hi Hans-Rudolf, I understand what you mean, but i think i am unable to do this. I am happy that i get an instance running in a docker container. I am also not sure if the parts in the galaxy wiky, which explain how to do this completely translate to docker... I have seen that there are other people out there which have the same issues. Would be great to get some input. However, I would also be happy to move the whole database and implement into new instance. Maybe someone can point me into the right direction?

can I just make a sudo -u postgres pg_dumpall > oldDB.out

and restore under the new folder?


ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Philipp.rathert30

Hi Philipp

I'm not an docker expert, so I can't comment on the docker specific issues you might run into... WRT the PostgreSQL dump command: Instead of dumping the whole PostgreSQL instance, I would just dump the galaxy database:

pg_dump -U <user> -d <database> -b -f oldDB.out

And then restore this database in your new PostgreSQL instance,


ADD REPLYlink written 2.0 years ago by Hotz, Hans-Rudolf1.7k

Hi Hans-Rudolf,

as I said, I am really a newbie (wetlab scientist). I think the user will be galaxy, but where do I find the name of the galaxy DB? and how do I restore this in the new instance?

ADD REPLYlink written 2.0 years ago by Philipp.rathert30

The name of the galaxy DB is the one you specified in the galaxy.ini of your instance at the line "database_connection = postgres://user:passwd@locahost/DBNAME?host....." ;) "

ADD REPLYlink written 2.0 years ago by christophe.habib340
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