Some questions (maybe for tomorrows morning round)...
# wg-container-conversion-task-force
j
Some questions (maybe for tomorrows morning round): 1. How can we retrieve the conda-lock files with wave? I cannot find a command that creates them, nor does there seem to be a logic to the urls (that I could find out). From the blog post :
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containers:
    docker:
        linux_amd64:
            name: <http://community.wave.seqera.io/library/fastqc:0.12.1--5cfd0f3cb6760c42|community.wave.seqera.io/library/fastqc:0.12.1--5cfd0f3cb6760c42>
            build_id: 5cfd0f3cb6760c42_1
            scan_id: 6fc310277b74
        ...
    singularity:
       ...
    conda:
        linux_amd64:
            lock file: <https://wave.seqera.io/v1alpha1/builds/5cfd0f3cb6760c42_1/condalock>
            ...
The url ttps://wave.seqera.io/v1alpha1/builds/5cfd0f3cb6760c42_1/condalock seems to be created based on
build_id
but it is not available.
m
because that build id is for docker I think. tried it manually following https://seqera.io/blog/ensuring-consistent-behavior-across-conda-and-docker-environments-with-wave/ and it worked
j
Ahhh! 💡 Only if you explicitly use
-o
in your wave command, will you see this:
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$ wave --conda-file modules/nf-core/fastqc/environment.yml --freeze --platform linux/arm64 -o yaml
buildId: bd-df99cb252670875a_2
cached: true
containerImage: <http://community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a|community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a>
freeze: true
mirror: false
requestId: 4d20bf525f4d
scanId: sc-b5913ed5d42b22d2_17
targetImage: <http://community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a|community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a>
Versus what we tried so far:
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$ wave --conda-file modules/nf-core/fastqc/environment.yml --freeze --platform linux/arm64        
<http://community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a|community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a>
e
Probably that will solve my issue as well then..no way to get condalock links through seqera containers then? Just by command line?
m
you get the build_id from the containers page
and then can resonstruct the url with
<https://wave.seqera.io/v1alpha1/builds/${build_id}/condalock>
👆 1
e
I got that, but later it seems like the condalock is unavailable
j
you can build the url by inserting your
build_id
and that gets you a download
e
Alright
j
you might have to run the other command first, but not sure
e
I think this is what I did and still get problems
m
do you have a url?
e
There is a PR i tagged you Mathias, for drugresponseeval..it should be there
e
m
I can download both conda lock files. Or do you mean something else?
e
I thought it was tied to the error, but it seems you replied to that already. Glad the links are fine! :D