Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
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
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Great, glad it's working again, especially since I wasn't having any great ideas other than the cache being out of date regarding that null, heh.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?
Dannon
@dannon
Is it a safe assumption that since this is an 18.04 machine it's not a production server, and more of a test? If so, then yeah, I'd say just wait a bit. Not worth wrangling a downgrade to 9.0, if that's even going to work.
moveisi
@moveisi
Well, yes it is not a production server (yet). So I can wait and at some point, I assume I should fetch the git clone to get your changes, which would be great!
Dannon
@dannon
Yes, exactly
moveisi
@moveisi
Perfect
Nicola Soranzo
@nsoranzo
@jmchilton The files in the directory are found using os.walk() in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/data_fetch.py#L218 , so there is not deterministic
galaxybot
@galaxybot
[mrscribe] Title: galaxy/data_fetch.py at dev · galaxyproject/galaxy · GitHub (at github.com)
John Chilton
@jmchilton
Yeah - I think we need to recursively sort that nested array items after the walk is complete. I can create an issue for that
Ordering is very important downstream from this function - so that function should be deterministic I think.
Jacob
@JacobAdelstein_twitter
Hello all, I am trying to map RNA data with BWA and I have executed the process. Unfortunately, the process must be in some kind of queue and it has said 'this job is waiting to run' for the last few hours. Does anyone have an time estimate on how long it will take for my map to complete?
This is my first time mapping the data so I'm just hoping for an idea
Dannon
@dannon
@moveisi: To follow up, I'm seeing the same error here on that rebuilt 1804 VM, so we should be able to get a fix out.
Dave B.
@davebx
sweet, double confirmed
moveisi
@moveisi
@dannon Great! Do you have any idea about the timing?
Dannon
@dannon
Not sure yet. I'll make a github issue to track it though.
moveisi
@moveisi
Perfect!