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Fail to automatically pulling Docker image in HPC environment (UPPMAX) #3

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DiegoBrambilla opened this issue Nov 15, 2019 · 0 comments

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@DiegoBrambilla
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The current version of the dev branch (commit 93d52a6) fails to build the default Docker image, namely in Creating the SIF file. Theissue can be reproduced by running (on UPPMAX):
nextflow run bioatlas/ampliflow -r dev -profile test,uppmax --trunclenF 150 --trunclenR 150 --nsamples 4 --taxa_db GTDB
Notably, this problem is unprecedented and so far only occurred with the docker image docker://diebra/ampliflow:dev .
As of now, the Docker image needs to be pulled manually with the command:
singularity pull --name diebra-ampliflow-dev.img docker://diebra/ampliflow:dev
and run it in the directory you specified for the variable $NXF_SINGULARITY_CACHEDIR.
You can either export such variable (thus making it available only for the duration of the current session):
export NXF_SINGULARITY_CACHEDIR=$HOME/.singularity
or set it into .bashrc / .bash_profile

@DiegoBrambilla DiegoBrambilla changed the title Fail in automatically pulling Docker image in HPC environment (UPPMAX) Fail to automatically pulling Docker image in HPC environment (UPPMAX) Nov 15, 2019
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