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Add fallback command for micromamba #4302

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merged 15 commits into from
Oct 26, 2024
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bentsherman
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Close #4161

Tested with micromamba image:

$ docker run --rm -it mambaorg/micromamba:1.4.9 -- bash
(base) $ command -v conda && (conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }') || (micromamba info | grep "env location :" | cut -d : -f 2)
 /opt/conda

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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@jemma-nelson
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Note that this PR only addresses the micromamba info invocation in point 2 of this comment:
#4161 (comment)

Another change would required to address point 1, the micromamba create --yes flag.

(I'm neutral on how y'all handle this, just want to make sure its clear).

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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pditommaso commented Dec 2, 2023

We are going to deprecate the support for Micromamba #4464. Therefore closing w/o merging

@ewels
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ewels commented Oct 23, 2024

Reopening, as not sure we should remove Mamba just yet, at least until conda/conda#13037 is solved.

@ewels ewels reopened this Oct 23, 2024
@pditommaso
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@jorgee avoid the fallback approach can be a mess to debug, there should be a separate command when the micromamba flag is set

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jorgee commented Oct 24, 2024

@jorgee avoid the fallback approach can be a mess to debug, there should be a separate command when the micromamba flag is set

I have pushed new changes with this modification. I think it is ready

jorgee and others added 3 commits October 25, 2024 15:26
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
@jorgee jorgee requested a review from pditommaso October 25, 2024 15:01
@pditommaso pditommaso merged commit 1243130 into master Oct 26, 2024
22 checks passed
@pditommaso pditommaso deleted the 4161-micromamba-info-command branch October 26, 2024 21:08
alberto-miranda pushed a commit to alberto-miranda/nextflow that referenced this pull request Nov 19, 2024

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com>
Co-authored-by: jorgee <jorge.ejarque@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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useMicromamba option doesn't work - generates Conda instructions instead.
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