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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e.g. builds for changesets that are already outdated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?
Dannon
@dannon
@JacobAdelstein_twitter If it says it's still waiting, restarting will only bump you to the back of the queue.
(so I wouldn't do that)
Martin Cech
@martenson
@JacobAdelstein_twitter that could easily happen during a busy queue times, if you restart it you will get back in the end
Jacob
@JacobAdelstein_twitter
Alright thanks everyone, I will keep it as is.
emily9542
@emily9542
Dear all. I am having a problem installing a tool called mutspec. It needs perl 5.18.1, which says it is installed but also has en error beside it "The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error." Could anybody suggest a place that I could find a fix? thanks in advance
Martin Cech
@martenson
I just checked and there is a fairly large queue atm.
John Chilton
@jmchilton
@jmchilton Do you know about the 'retry build after failure' on some of our test jobs?
I do not
galaxybot
@galaxybot
[clements] Hi All, just a reminder that * talk abstracts for GCCBOSC are due this Friday.* https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open
[mrscribe] Title: March 2018 Galaxy News (at galaxyproject.org)
[clements] And, we'll be announcing conference-subsidized childcare later this week. So, don't let that hold you back.
Martin Cech
@martenson
@jmchilton I will kill it for now
Nicola Soranzo
@nsoranzo
Is there any good reason to show composite datatypes in the Type dropdown of the upload window when the Regular tab is selected?
Martin Cech
@martenson
probably not
Nicola Soranzo
@nsoranzo
@emily9542 I'd suggest to the tool authors to use Conda for tool dependencies instead of ToolShed packages
Micropathology
@Micropathology
Is there anything indicative of all newly installed tools giving command not found errors?
selten
@selten
Apart from running the tool that would fail?
or the i button showing 'command not found'?
Micropathology
@Micropathology
Sorry that read wrong. I meant is there an obvious problem which would cause all newly installed tools to produce this error?
Marius van den Beek
@mvdbeek
Something wrong with your conda installation ? Anything in the logs ?
Micropathology
@Micropathology
I checked the galaxy logs and its saying that python and conda need to be updated. I'm not sure why this is suddenly the case. The only thing I have done recently to the cluster is to resize the partition.
Martin Page
@doomedramen
Hey all, got a bug question for you, I know you love them
Marius van den Beek
@mvdbeek
shoot
Martin Page
@doomedramen
Adding datasets to galaxy ("from path"), when selecting "Link files instead of copying" I had assumed it would make a symbolic link...
Marius van den Beek
@mvdbeek
@Micropathology what exactly are the logs saying ?
Martin Page
@doomedramen
turns out this is not the case
Marius van den Beek
@mvdbeek
it should be, unless you also checked line ending conversion
Martin Page
@doomedramen
I dont see an option for that here