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Inconsistency between Dockerfiles and singularity images #59

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fgypas opened this issue Feb 7, 2020 · 0 comments
Open

Inconsistency between Dockerfiles and singularity images #59

fgypas opened this issue Feb 7, 2020 · 0 comments
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@fgypas
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fgypas commented Feb 7, 2020

When we pull a docker image with singularity that contains information such as:

# VARIABLES
ARG WORKDIR="/home/container/"
ARG USER="USER"
ARG GROUP="GROUP"
ENV PATH="${WORKDIR}:${PATH}"

# CREATE USER
RUN groupadd -r ${GROUP} && useradd --no-log-init -r -g ${GROUP} ${USER}

# SET ENVIRONMENT
WORKDIR ${WORKDIR}
RUN chown -R ${USER}:${GROUP} ${WORKDIR} && chmod 700 ${WORKDIR}
USER ${USER}

singularity cannot convert it properly to an image and it returns error like:

Singularity: action-suid (U=0,P=480)> Home directory is not owned by calling user: /tmp/repo/rnaseqpipeline/tests/test_integration_workflow

ERROR  : Home directory is not owned by calling user: /tmp/repo/rnaseqpipeline/tests/test_integration_workflow
Singularity: action-suid (U=0,P=480)> Retval = 255

Tested with singularity v2.6.1

How should we handle this?

@fgypas fgypas added the help wanted Extra attention is needed label Feb 7, 2020
@fgypas fgypas added bug Something isn't working question Further information is requested labels Feb 7, 2020
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