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John Chilton
@jmchilton
Sounds like a bug - the ftp directory should be sorted on the server before creating a collection I think
moveisi
@moveisi
I am having trouble installing Galaxy with PostgreSQL on an Ubuntu 18.04 system.
Galaxy runs using SQLite with no problems. However, when I try to connect to PostgreSQL instead I get errors from "psycopg2". It says:
File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/psycopg2/init.py", line 50, in <module>
from psycopg2._psycopg import BINARY, NUMBER, STRING, DATETIME, ROWID
ImportError: /home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/psycopg2/.libs/./libresolv-2-c4c53def.5.so: symbol __res_maybe_init version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
galaxybot
@galaxybot
[nekrut] @jmchilton: can you point me to your hierarchical collection upload PR. I cannot find it for some reason
moveisi
@moveisi
@jmchilton: sorry, if you are asking me, I am not sure which collection you mean.
John Chilton
@jmchilton
@moveisi I was responding to @nsoranzo - sorry about that
galaxybot
@galaxybot
[nekrut] @dave_b @nate: https://github.com/usegalaxy-eu/usegalaxy-eu-tools
[mrscribe] Title: GitHub - usegalaxy-eu/usegalaxy-eu-tools: List of tools included in (at github.com)
John Chilton
@jmchilton
@nekrut Frontend : galaxyproject/galaxy#5365 , backend : galaxyproject/galaxy#5220 , training : galaxyproject/training-material#676
galaxybot
@galaxybot
[mrscribe] Title: Rule-based Uploader / Builder by jmchilton · Pull Request #5365 · galaxyproject/galaxy · GitHub (at github.com)
[nekrut] TX!
John Chilton
@jmchilton
@moveisi I really don't know about your issue, this is just a stab in the dark but it might be worth trying: ./.venv/bin/pip uninstall psycopg2 && ./.venv/bin/pip install --no-cache-dir --no-binary psycopg2
In case the wheel we distribute with Galaxy for that dependency doesn't work - I think this variant should try to build one from source from PyPI. I'm not sure thouhg
moveisi
@moveisi
@jmchilton: that is great :smile: I will try it and get back to you ...
Dave B.
@davebx
seconding @jmchilton, I sometimes encounter that issue and that's how I resolve it
Rajeev Vikram
@darkrid_twitter
@dannon yeah checked it Thanks.
Dannon
@dannon
That fixed it?
Rajeev Vikram
@darkrid_twitter
Haven't yet cleaned out
Dannon
@dannon
Ahh, k, let me know if that doesn't fix it and we can try to debug more.
Rajeev Vikram
@darkrid_twitter

Yeah. still the same error.

https://usegalaxy.org/user/logout?session_csrf_token=null

galaxybot
@galaxybot
[mrscribe] Title: Galaxy | (at usegalaxy.org)
Dannon
@dannon
Ah-ha! How is that session_csrf_token null...
Rajeev Vikram
@darkrid_twitter
yep. its the null ....lol
Rajeev Vikram
@darkrid_twitter
Seems Fixed :clap:
Dannon
@dannon
Awesome. Cache clean and reload did it?
Rajeev Vikram
@darkrid_twitter
I suppose so.
Dannon
@dannon
Great, glad it's working again, especially since I wasn't having any great ideas other than the cache being out of date regarding that null, heh.
Rajeev Vikram
@darkrid_twitter
Now, only if galaxy server starts to run my jobs, the lag is extreme and I have some single cell RNA analysis going on. haha
Thanks.
Dannon
@dannon
Sure! Someone said there was a backup yesterday after the server updates, may just take a few to get moving.
moveisi
@moveisi

@jmchilton and @davebx thanks a lot for your help!
I could install psycopg2 with --no-cache-dir --no-binary as you recommended.
However, when I ./run.sh Galaxy again, it uninstalled my freshly installed psycopg2, and download and installed the binary version again! Any suggestions?

...
Collecting psycopg2==2.6.1 (from -r /dev/stdin (line 1))
Downloading https://wheels.galaxyproject.org/packages/psycopg2-2.6.1-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB)
100% |████████████████████████████████| 2.0MB 553kB/s
Installing collected packages: psycopg2
Found existing installation: psycopg2 2.7.4
Uninstalling psycopg2-2.7.4:
Successfully uninstalled psycopg2-2.7.4
Successfully installed psycopg2-2.6.1
...

Dave B.
@davebx
@moveisi oh yeah, you'll want to add psycopg2==2.6.1 to the end of the pip install command
moveisi
@moveisi
@davebx sure I'll try :smile:
moveisi
@moveisi

@davebx Is it possible to get Galaxy work with PostgreSQL 10?
I am running Ubuntu 18.04 (with PostgreSQL 10 as the default verion). When I try

./.venv/bin/pip install --no-cache-dir --no-binary psycopg2 psycopg2==2.6.1

it says:

Error: could not determine PostgreSQL version from '10.2'

Dave B.
@davebx
that is a good question, I've only tried with postgres 9.x
Dannon
@dannon
Is 10.x the default in 18.04?
Actually, I was tinkering with an 18.04 VM here, let me see if I'm having the same problem there.
moveisi
@moveisi
Yes, apt install postgresql gives you version 10
@dannon I appreciate it!
Nicola Soranzo
@nsoranzo
Time to update our requirement and wheel?
Dave B.
@davebx
@dannon looks like yes
Dannon
@dannon
Yeah, might be if this is going to be a problem for all 18.04.
moveisi
@moveisi
so do I downgrade my postgresql to 9?
Dave B.
@davebx
let's hope it's not a problem for backward compatibility
Dannon
@dannon
D'oh. I deleted the budgie vm I was testing. If dave's seeing it, too, then it sounds like 'bug confirmed', though.
Dave B.
@davebx
confirmed in the sense that this metapackage depends on postgres 10: https://packages.ubuntu.com/bionic/postgresql
galaxybot
@galaxybot
[mrscribe] Title: Ubuntu – Details of package postgresql in bionic (at packages.ubuntu.com)
Dannon
@dannon
Oh, got it. I'll rebuild that VM real quick and confirm the wheel blows up for me, too, then.
Dave B.
@davebx
I've yet to upgrade my dev boxen to 18.04, so I can't directly confirm
Matthew Spelchak
@tizzir
I've updated galaxyproject/galaxy#5645, it had a bunch of unrelated files in it, whoops! Should be a lot easier to read now.
moveisi
@moveisi
@dannon oh great, so if you might be fixing this soon, I just wait a bit until it is fixed. Is that what you would recommend too?