Data intensive science for everyone. http://galaxyproject.org | Use now! http://usegalaxy.org
but the PJAs should work for all kinds of tags
btw a colleague of mine asked me recently why he can't name outputs in the tool form -- maybe tool form PJAs would be worth thinking about ?
maybe circleci is a better fit for this
although repetition is not exactly uncommon in CI. =)
Look for
py3_addons in https://github.com/galaxyproject/galaxy/blob/dev/.travis.yml for macro syntax.
@nsoranzo: oh using standard YAML references?
@natefoo Yes (I think)
Is that feasible on https://github.com/galaxyproject/starforge-recipes ?
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.
not sure if i saved that anywhere either
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!
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]
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?
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?
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 ?
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
@mvdbeek I have a fix for the pipenv issue, PR coming soon