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Dannon
@dannon
So rsync with --include and --exclude reproduces my gulp globbing copy perfectly, but... It requires rsync.
John Chilton
@jmchilton
@bgruening Batching regular Galaxy jobs should be feasible - that would allow a lot of benefits of Galaxy datatypes, collections, runner backends.
It is a big task in its own right - but we need the feature I think
Nicola Soranzo
@nsoranzo
We have 2 uWSGI processes (+ the master) and in the last week we had 10 occurrences of a worker being killed because of the memory limit
@dannon I think I've missed why we cannot use gulp directly.
Dannon
@dannon
We could, but I thought folks wanted a non-js integration for the staging. Let me reread.
Nicola Soranzo
@nsoranzo
@jmchilton Another idea we have is to split the big collection in a few smaller ones, run the tool on each, and then merge them again, as a workaround.
Is there a tool to extract the element identifiers of all datasets in a collection?
John Chilton
@jmchilton
I’m not sure - I can’t think of a way to do it with the stock tools but I’m not sure what is available in the shed
Nicola Soranzo
@nsoranzo
I haven't found one on the TS, but should be pretty easy for a list collection.
John Chilton
@jmchilton
You could break up the collection a little more directly with Apply Rules in 18.05 - but I suppose you are still on 18.01
Nicola Soranzo
@nsoranzo
Yep, we will upgrade after GCCBOSC, too busy now
John Chilton
@jmchilton
Completely understand
Martin Cech
@martenson
looking at dev list 18.01 is not that bad :)
Nicola Soranzo
@nsoranzo
It's serving us well!
Nate Coraor
@natefoo
@RJMW: sorry. so slurm supports specifying multiple partitions by specifying them as a comma separated list to -p. i have not tested this with slurm-drmaa though.
Nicola Soranzo
@nsoranzo
@jmchilton galaxyproject/tools-iuc#1939
galaxybot
@galaxybot
[mrscribe] Title: Add tool to extract element identifiers from a list collection by nsoranzo · Pull Request #1939 · galaxyproject/tools-iuc · GitHub (at github.com)
Stephen Ficklin
@spficklin
Hello! is there an API function for sharing a workflow? We can do it via the web interface but we cna't seem to find this in the API docs.
Nicola Soranzo
@nsoranzo
Unfortunately no, see galaxyproject/galaxy#1630
galaxybot
@galaxybot
[mrscribe] Title: Expose workflow sharing in API · Issue #1630 · galaxyproject/galaxy · GitHub (at github.com)
Stephen Ficklin
@spficklin
Thanks @nsoranzo . So, we'll just approach it by importing the workflow then. Thanks
Martin Cech
@martenson
@Delphine-L I made an issue for what you reported: galaxyproject/galaxy#6331
galaxybot
@galaxybot
[mrscribe] Title: fix collection hid inconsistency · Issue #6331 · galaxyproject/galaxy · GitHub (at github.com)
Kyu Sang Han
@kukionfr
Hi, i am having trouble with launching local galaxy instance
when I run "sh run.sh", it randomly throws me an error that says
it cannot uninstall certifi. I understand why it cannot uninstall, and how to get around it
but I haven't find the absolute solution for this problem as I see it continues to occur occasionally
the way I get around this is by manually deleting certifi from site-packages and reinstalling it
Marius van den Beek
@mvdbeek
@kukionfr does your galaxy setup use its own virtualenv or is this shared systemwide or is it a conda environment ?
the recommended way is the have a dedicated virtualenv for galaxy (.venv in the galaxy dir by default), and then this environment will only be changed if you update galaxy
Kyu Sang Han
@kukionfr
oh i forgot to use virtualenv. just ran sh in systemwide terminal
Marius van den Beek
@mvdbeek
that should still use a local virtualenv, unless you also have conda on your path
you can see this at the very beginning when you run sh run.sh
Kyu Sang Han
@kukionfr
yes, it says running virtualenv
what i did is
i cloned new galaxy using, $ git clone -b release_18.05 https://github.com/galaxyproject/galaxy.git
galaxybot
@galaxybot
[mrscribe] Title: GitHub - galaxyproject/galaxy: Data intensive science for everyone. (at github.com)
Kyu Sang Han
@kukionfr
and did sh run.sh
everytime I reboot my computer, I started local galaxy using sh run.sh
then one day it threw me that certifi error
I wonder why
Marius van den Beek
@mvdbeek
so does this happen every time or only when you update galaxy? what is the exact message ?
Kyu Sang Han
@kukionfr
I don't know what update galaxy means to be honest.
Installing collected packages: certifi, pyparsing
Found existing installation: certifi 2018.4.16
Cannot uninstall 'certifi'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
animation-mac-pro-two:galaxy wirtzlab$ pip uninstall certifi
Cannot uninstall 'certifi'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
this is the message
and the very beginning is like this:
animation-mac-pro-two:galaxy wirtzlab$ sh run.sh
There is no existing Galaxy virtualenv and Conda is available, so we are skipping virtualenv creation. Please be aware that this may cause missing dependencies.
Requirement already satisfied: pip>=8.1 in /Users/wirtzlab/miniconda2/lib/python2.7/site-packages (10.0.1)
so i guess, there is conda ?
Marius van den Beek
@mvdbeek
yes