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bgruening / docker-galaxy

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy
MIT License
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Docs for upgrading postrgres don't work #527

Closed tdudgeon closed 5 years ago

tdudgeon commented 5 years ago

Th instructions for upgrading postgres in 19.05 don't work.

1) The command docker exec galaxy bash needs to be docker exec -it galaxy bash

2) The command pg_dumpall --clean > /export/postgresql/9.3dump.sql fails with:

pg_dumpall: could not connect to database "template1": FATAL:  role "root" does not exist

I also tried as galaxy user but that fails with permission denied error

bgruening commented 5 years ago

mh, can you run it as postgres user?

dpryan79 commented 5 years ago

Create the output folder as root and give the galaxy user write permissions. Then pg_dumpall should work.

tdudgeon commented 5 years ago

sorry, yes I had missed the su postgres command, but that still didn't work as postgres user can't write to /export/postgresql. If you create a new dir and owned by postgres then you can do the dump to there as the postgres user.

tdudgeon commented 5 years ago

2 other problems I found:

  1. the for f in *; do echo $f; diff $f ../../galaxy-data-old/galaxy-central/config/$f; read; done didn't wok for me. It just hung and did nothing.
  2. if the upgrade also needs the postgres upgrade it's not really clear from the docs in which order things should be done in,
abretaud commented 5 years ago

postgres user can't write to /export/postgresql

On my instance /export/postgresql is owned by postgres user, it's not the case for you? Which version are you upgrading from? Is /export mounted from a local path?

the for f in *; do echo $f; diff $f ../../galaxy-data-old/galaxy-central/config/$f; read; done didn't wok for me. It just hung and did nothing.

Strange, are there the expected xml files in ./ and ../../galaxy-data-old/galaxy-central/config/?

tdudgeon commented 5 years ago

OK, so I can write to the /export/postgresql dir when doing the dump now (using the upgraded environment) so I'm not sure what was wrong. I was upgrading from 19.01.

And yes, there are the expected files in the galaxy-central/config dir.