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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!
Dannon
@dannon
@moveisi: galaxyproject/galaxy#5696 for tracking the issue, if you're interested.
galaxybot
@galaxybot
[mrscribe] Title: psycopg2 wheel failure on ubuntu 18.04 · Issue #5696 · galaxyproject/galaxy · GitHub (at github.com)
Dannon
@dannon
As a quick fix, you can apply https://gist.github.com/5f512f0210e53ea9116ed6c3f9fd6052 and it should work fine.
galaxybot
@galaxybot
[mrscribe] Title: gist:5f512f0210e53ea9116ed6c3f9fd6052 · GitHub (at gist.github.com)
Nicola Soranzo
@nsoranzo
That gist is a bit unreadable @dannon
Dannon
@dannon
Yeah, already updating it. It's git diff --color causing it.
Jacob
@JacobAdelstein_twitter
Basically my question is, is it supposed to take hours for Galaxy to run a BWA map?
Dannon
@dannon
@JacobAdelstein_twitter Not usually, no, but the queue can occasionally get backed up.
Nicola Soranzo
@nsoranzo
@jmchilton Not sure what would be the correct behaviour in case of nested directories
Dannon
@dannon
If you always used sorted(dirs) and sorted(files) it'd always come out the same, right?
Nicola Soranzo
@nsoranzo
My question would be: do we want to sort by the full (sub)path or the file name?
John Chilton
@jmchilton
Not the file name - each level should be sorted by the name of that level - so I think @dannon's suggestion is correct
I think anyway...
Nicola Soranzo
@nsoranzo
OK, that fixed the test for me!
Dannon
@dannon
Nice!
Martin Cech
@martenson
@jmchilton Do you know about the 'retry build after failure' on some of our test jobs?
I think it does not respect ghprb rules and creates many unnecessary builds
e.g. builds for changesets that are already outdated
Jacob
@JacobAdelstein_twitter
@dannon I started the BWA map a good 4 hours ago. It says it is still waiting. Do you suggest that I restart it?