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Nicola Soranzo
@nsoranzo
Look for py3_addons in https://github.com/galaxyproject/galaxy/blob/dev/.travis.yml for macro syntax.
Nate Coraor
@natefoo
right now over in galaxyproject/starforge-recipes it can build platform ones w/ matrix jobs out to linux and macos, 2.7, 3.4, 3.5, 3.6
@nsoranzo: oh using standard YAML references?
Nicola Soranzo
@nsoranzo
Speaking of which, we need to build wheels for the recently-released uwsgi 2.0.17.1 , building the previous 2.0.17 on Fedora 28 is broken due to its new glibc
@natefoo Yes (I think)
Nate Coraor
@natefoo
yeah it should be possible in its current state
Helena Rasche
@erasche
wrote a queue time SQL script? I'm pretty sure @natefoo sent me one at one point, but, here's a rewrite bceause I couldn't find that one:
CREATE TEMPORARY TABLE temp_queue_times AS
select
    min(a.create_time - b.create_time) as queue_time
from
    job_state_history as a
inner join
    job_state_history as b
on
    (a.job_id = b.job_id)
where
    a.job_id in (select id from job where tool_id like '%"$1"%' and state = 'ok' and create_time > (now() - '3 months'::interval))
    and a.state = 'running'
    and b.state = 'queued'
group by
    a.job_id
order by
    queue_time desc
;
--
select
    min(queue_time),
    percentile_cont(0.95) WITHIN GROUP (ORDER BY queue_time) as perc_95,
    percentile_cont(0.99) WITHIN GROUP (ORDER BY queue_time) as perc_99,
    max(queue_time)
from temp_queue_times;
("$1" because this was from a bash script and I forgot to replace that.BBut y'all get the idea.)
Looking at last 3 months of rna star jobs on our server:
 bash scripts/queue_time.sh rnastar
       min       |     perc_95     |     perc_99     |          max
-----------------+-----------------+-----------------+-----------------------
 00:00:08.007632 | 04:42:01.661542 | 10:59:26.373311 | 1 day 05:24:10.246863
ping @bgruening it's in galaxy's homedir.
Nate Coraor
@natefoo
yay!
not sure if i saved that anywhere either
Marius van den Beek
@mvdbeek
Cool, the build triggers are working. If you want to run additional python3 tests on a PR (api, framework,integration) comment with @galaxybot test py3
Jennifer Hillman-Jackson
@jennaj
usegalaxy.eu error reported at Biostars. I'm not familiar with the tool and don't have admin access to look at their error in detail. Could someone from EU team help? https://biostar.usegalaxy.org/p/29168/ Tx!
Marius van den Beek
@mvdbeek
I think https://bugs.python.org/issue21161 might be a problem for cheetah templates that use list comprehensions on python 3 :(
or at least for list comprehensions that reference variables from the surrounding scope, like [i for i in $var1 if i in $var2]
Vahid
@VJalili
@nsoranzo when I remove a pinned required from dependencies/pipfiles/default/pinned-requirements.txt and run make update-dependencies, the command then empties the dependencies/pipfiles/default/pinned-requirements.txt file. Is this an expected behavior?
Vahid
@VJalili
I think it is due to some conflicts in the dependencies.
Nicola Soranzo
@nsoranzo
It is surely not expected. There should be quite a bit of verbose output from pipenv though.
tomsuntom
@tomsuntom
I am trying to run Galaxy on my mac but when I type in "sh run.sh" it says "activating virtualenv at .venv
Collecting pip>=8.1
Could not find a version that satisfies the requirement pip>=8.1 (from versions: )
No matching distribution found for pip>=8.1". Anyone know how to fix it?
Nicola Soranzo
@nsoranzo
What system is it?
Marius van den Beek
@mvdbeek
@VJalili @nsoranzo I've been having the same issues. The main problem is the genomospace cleint which pins an old boto. If this ends up in a conflict I also get an empty dependencies/pipfiles/default/pinned-requirements.txt
Christophe Antoniewski
@drosofff

Hi, I did not notice immediately, but I think that since we have updated to release_18.05, the files that are ftp-uploaded by our instance's users are not seen anymore in the "Choose FTP files" panel (warning "Your FTP directory does not contain any files."). We are still using the .ini format for the galaxy config files; the galaxy log says

galaxy.webapps.galaxy.api.remote_files WARNING 2018-08-22 13:02:33,773 [p:31389,w:2,m:0] [uWSGIWorker2Core4] The directory "'/home/galaxy/galaxy-dist/database/ftp/drosofff@gmail.com'" does not exist.

which is not true !

Any new variable to adjust with release_18.05 ?

Marius van den Beek
@mvdbeek
Any chance that '/home/galaxy/galaxy-dist/database/ftp/drosofff@gmail.com' has single quotes in the galaxy.ini file ?
The string template is "The directory \"%s\" does not exist.", if you fill that with a path you should get 'The directory "/some/path" does not exist.'
This is dynamically generated anyway, so I guess that shouldn't be the issue
Marius van den Beek
@mvdbeek
do you see directory 'home/galaxy/galaxy-dist/database/ftp/drosofff@gmail.com' is a symlink to a location not on the whitelist' in the logs ?
Marcel Kempenaar
@mkempenaar
Hi guys, question; I've deleted + purged a large number of users from our Galaxy server. which of the cleanup scripts do I need to run to delete all their data from disk? (spoiler: none worked)
Nicola Soranzo
@nsoranzo
@mkempenaar See galaxyproject/galaxy#6603
@mvdbeek I have a fix for the pipenv issue, PR coming soon
Marius van den Beek
@mvdbeek
awesome, thanks @nsoranzo !
Nicola Soranzo
@nsoranzo
I should say a workaround
Marcel Kempenaar
@mkempenaar
@nsoranzo concluding that there is no easy method of actual deleting the files that are still assigned to deleted + purged users?
Instead of un-deleting + impersonating?
side question: there is about 300GB in database/tmp, are they save to remove manually?
Marius van den Beek
@mvdbeek
if nothing is using files in database/tmp , yes
we need to also delete histories when deleting a user, then the cleanup scripts should work, I was going to look into this for this release cycle
Marcel Kempenaar
@mkempenaar
Thanks.
Is there a way of performing @AjitPS latest comment in the database? That would be a preferable solution for now.
Marius van den Beek
@mvdbeek
Sure, mark histories owned by the deleted user as deleted
you don't need to set them to userless, deleted is better
Marcel Kempenaar
@mkempenaar
Thanks, going to give that a try.
Marcel Kempenaar
@mkempenaar
What value would I use for user_id in the history table to set it to userless?
Marius van den Beek
@mvdbeek
why do you want to do that, does deleting not work ?
for real difficult post-mortem cases it would be good to know who produced a history, even if you can't restore the data
which you can't if you set it to userless
Nicola Soranzo
@nsoranzo
@mkempenaar You can use tmpreaper (or tmpwatch) to clean database/tmp
Marcel Kempenaar
@mkempenaar
For one user, all his histories are already flagged as deleted, however he still has 15GB in the disk_usage column.
Marius van den Beek
@mvdbeek
ignore this column, it is often not accurate and needs to be updated out of band, or by explicitly logging out the user
the important question is wether the datasets have been deleted