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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Ghost
@ghost~5772e7e2c2f0db084a206e1b
tests are running, I’ll let you know
this one seems to work
not sure if it’s the new one though
ah
it might have been the multi-build container that was broken
which I fixed by bumping the samtools version
sorry
Björn Grüning
@bgruening
all good :)
Ghost
@ghost~5772e7e2c2f0db084a206e1b
I’m rewriting the involucro part of mulled-build in python, couldn’t figure out how to capture container output and use it in a subsequent step… if I fdo this we could also produce proper docker files using the multi-stage strategy. would that be something worth publishing somewhere ?
Björn Grüning
@bgruening
?
You are rewriting involucro?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
replacing
it’s just silly complex
and unmaintained
Björn Grüning
@bgruening
it is not unmaintained
and this is what is creating all our containers
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Björn Grüning
@bgruening
I don't think its a good idea to change it now
Ghost
@ghost~5772e7e2c2f0db084a206e1b
it doesn’t do anything you can’t do in a single docker build command
it’s from a time when we didn’t have multi-stage builds
Björn Grüning
@bgruening
you see there was a recent release in October
Ghost
@ghost~5772e7e2c2f0db084a206e1b
and the last one before that in 2016
since then I’ve had an open issue and hosted the osx version Galaxy uses
Björn Grüning
@bgruening
OSX version?
sorry, was not aware of this
Ghost
@ghost~5772e7e2c2f0db084a206e1b
Björn Grüning
@bgruening
have you tried the new release?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
no
but why use this overly complex thing that isn’t designed to interact and capture container output
?
if we just template out a dockerfile we can do the same for singularity, giving us on-the-fly singularity builds without needing docker, that would be another advantage
and we don’t need host mounts either that aren’t properly clean up
there’s lot’s of advantages to be had if we simplify this
Ghost
@ghost~5772e7e2c2f0db084a206e1b
this wouldn’t change anything whatsoever in how you use the mulled-build ecosystem
same commandline flags etc
and we can also template out the ENV vars that conda activate puts into the environemnt
Björn Grüning
@bgruening
I'm not worried about that. Many people complained about the lua stuff, so there is probably some appeal to use multi-stanged-build - I guess lua was a wrong choice. I just think its a bad timing. This really needs to be tested carefully before we can roll this out. This has a large impact to not only our ecosystem.
Ghost
@ghost~5772e7e2c2f0db084a206e1b
the lua file is quite simple in what it does, I will produce tests for all cases
Björn Grüning
@bgruening
Sorry, I'm in an EOSC meeting, I can not concentrate enough on this topic as it deserves
Ghost
@ghost~5772e7e2c2f0db084a206e1b
alright, no worries
Ghost
@ghost~5772e7e2c2f0db084a206e1b
let’s see, maybe I can save myself the work: involucro/involucro#73
M Bernt
@bernt-matthias
Is there any convention if characters in the help attribute should/need to be quoted (e.g. & < ...)?
Damn I need to quote them here :) lol
Ghost
@ghost~5772e7e2c2f0db084a206e1b
I guess it depends how many of them they are
if it’s utterly unreadable I’d create a token
Nicola Soranzo
@nsoranzo
Use CDATA?
Ghost
@ghost~5772e7e2c2f0db084a206e1b
can’t do that within an attribute (AFAIK)
but it’d work in a token
Nicola Soranzo
@nsoranzo
<param name="foo" type="text" value="">
    <help><![CDATA[
I'm using weird stuff here >&<
    ]]></help>
</param>
I think that should work, if it is worth