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Dannon
@dannon
(that's external key/token, but I'd expect handling should be similar)
Matt Chambers
@chambm
@bgruening not quite :/ It'd need to try inferring rules automatically. But it would be really cool if it could do that and then present its clusters (collections) to the user for tweaking. My approach made occasional mistakes due to string distance quirks
Martin Cech
@martenson
@chambm to me your usecase seems like a need for 'decision' points in a workflow
there was some work done in that, but I am not sure whether it is ready yet
with that you could maybe represent it as a single workflow that the user 'customizes' at runtime
without actually changing the underlying wf definition
Matt Chambers
@chambm
yes, if the built-in workflow system allowed conditionals, that would totally obviate my need for workflow generation
Martin Cech
@martenson
@mvdbeek @jmchilton I remember seeing some progress here, could you weigh in please? ^
e.g. galaxyproject/galaxy#6664
Björn Grüning
@bgruening
@chambm this rule-based uploader can be used in workflows if that is your use-case
pvanheus
@pvanheus
so all we need is for CWL 2.0 to come out with support for conditionals and for Galaxy to support CWL - and then @chambm's problem is fixed :)
but yes right now there is no "natural" way to do this
does the tool know the username at least of the user that is running it?
najitaleb
@najitaleb
galaxyproject/galaxy#2340 is there anyone familiar with users_shared_with and what arguments it needs so that it can be changed through API?
Matt Chambers
@chambm
@pvanheus Yes. My colleague said he solved this problem already actually. Uses the master API key from Galaxy config to create or lookup the API key for the executing user.
pvanheus
@pvanheus
@chambm and then you can pass that key into the tool via an environment variable set in job_conf.xml
Dannon
@dannon
@jmchilton I can't find it now, but I thought you implemented a config option that'd allow future database versions. Did I just dream this up, or am I missing it in the code?
(so, I could run a database at 145 against 142 code without an actual downgrade, for example)
If I did just dream it up, it sounds like a nice dev feature...
John Chilton
@jmchilton
Yeah, PR needed some work. But I frequently wish it had been merged 😅
Martin Cech
@martenson
galaxyproject/galaxy#4670
Dannon
@dannon
Uhh. If you want any prodding, I would be more than happy, because this is driving me nuts! :)
Ahh, yeah, that's the one. Okay. At least I know I didn't just make it up!
pvanheus
@pvanheus
can someone help me debug this ImportError: cannot import name _remove_dead_weakref issue? as I recall it is a clash happening between Python in the conda environment used by the tool and the Python in the virtual env. I'm trying to reproduce it outside of Galaxy, but failing... and inside Galaxy I really don't know how to avoid it.
Jennifer Hillman-Jackson
@jennaj
Devs: Is there a way to limit selects to a single input dataset (only) that I missed? Please help with advice here if so: https://help.galaxyproject.org/t/param-showing-data-output-from-history-but-not-dataset-ie-multiple-outputs-nor-collections/180
John Chilton
@jmchilton
Your answer is essentially correct, there is no flag to disable that.
I'd be hesitant to add one as well.
Jennifer Hillman-Jackson
@jennaj
thanks @jmchilton -- @bgruening added something else but I think that expands in the UI. You both know better than me!
Martin Cech
@martenson
@nsoranzo did we manage to plug in the boto fix in galaxy?
I cannot find it
we are seeing it here: galaxyproject/galaxy#7078
which is 18.09
Martin Cech
@martenson
well we actually put it in dev
Martin Cech
@martenson
@jmchilton if you merge galaxyproject/galaxy#7092 7078 will pass I believe
John Chilton
@jmchilton
I've implemented a bot that just merges as me if I'm pinged here with PR number included in the message. Good news is, it seems to work so far!
Martin Cech
@martenson
I bet this message is from a bot too...
Björn Grüning
@bgruening
@jmchilton galaxyproject/galaxy-lib#87 - test this bot! - just kidding!
John Chilton
@jmchilton
Luckily it only works for PRs I haven't already commented on :sweat_smile:.
Björn Grüning
@bgruening
such a smart bot :)
galaxybot
@galaxybot
[hotdogs] is there a release that includes the client files already built?
Martin Cech
@martenson
@hotdogs: not since 18.09
Dannon
@dannon
Not 18.09 and after. Are you having trouble building them?
(should all be completely automatic now)
galaxybot
@galaxybot
[hotdogs] yeah, it's breaking trying to run gulp
Dannon
@dannon
Can you gist or otherwise share the exact error log?
galaxybot
@galaxybot
[hotdogs] I'd like to avoid having to install a mess of build deps
Dannon
@dannon
Yeah, you shouldn't have to install anything, it should all be self contained.
Galaxy boostraps up its own dependencies. There was one hitch, which I have since fixed, where if it detected a local nodejs/yarn it'd just use it.
galaxybot
@galaxybot
[hotdogs] https://gist.github.com/bldewolf/f9a2f1d56bfbd246eb5778c42b743fc6
Dannon
@dannon
Actually, yeah, if you can share the exact hash you're using too (git rev-parse HEAD) that's useful info.