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Questions tagged [apptainer]

Apptainer is a container environment and a successor to Singularity containers as a part of a rebranding. Apptainer is part of the Linux Foundation and the management organization's website may be found here: https://apptainer.org/

26 questions
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Use SSH key of host during Singularity/Apptainer build

When building a Singularity/Apptainer image from a definition file, is there a portable way to make a SSH key of the host system available during the build? To give some context: I have a definition file where in the %post section I'm cloning a…
luator
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Automatically source configuration when running Singularity container with "shell" command

I use a Singularity/Apptainer container (build from a definition file) to build the code of my project. The way I use it is to run the container with singularity shell my_container.sif such that my workspace is mounted in the container and then run…
luator
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Nextflow Singularity/Apptainer Command not Found

I have a nextflow workflow for which I am running with sge + apptainer profile using the command nextflow run main.nf -profile sge,apptainer but I am receiving the error line #: bwa: command not found I have tried running apptainer run workflow.sif…
1288Meow
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Docker to Apptainer/Singularity image for Julia application: manifest_usage.toml Read-only file system

I'm trying to create a docker image that could work also in singularity for the software Whippet ( https://github.com/timbitz/Whippet.jl ). The docker image works fine, but when I try to use it with singularity (singularity-ce version 3.9.5), It's…
Claudio Lorenzi
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Bind path in singularity using container environment variable

I have a singularity container built with a scientific filesystem app. I run the container with singularity run --app myapp image.sif and, accordingly, I have the environment variable SCIF_APPDATA=/scif/data/myapp set inside the container. I'd like…
Michele
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Apptainer. Input/output files/dirs outside the container

I need to run the software souporcell using apptaimer (or singularity 3.9.2) and a bash script. The script uses .bam, .tsv, .fa, i.vcf as input, as well as the files souporcell_latest.sif and souporcell_pipeline.py. I "connected" the inside and…
Lucas
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How to install Python or R in an apptainer?

I am new to docker and using apptainer for that. the def file is: firstApp.def: `Bootstrap: docker From: ubuntu:22.04 %environment export LC_ALL=C ` then I built it as follows and I want it to be writable (I hope I am not so naive), so I can…
m.i.cosacak
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How to make aliases of apptainer container tags?

Apptainer (and singularity) can interact with container registries, much like docker can. Common practice for these registries is to have a (semantic version) tag for each image pushed and maintain the tag "latest" to point to the most recent…
thegreatemu
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Docker container works well, but Singularity sif creates permission error

I created a Docker image that works as expected. I've provided the dockerfile and entrypoint file here on the off chance it's helpful. I can run through prokaregia.sh, the script the environment was designed to run, as expected with the following…
schmiggle
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How to modify temporary files when running apptainer interactivelly

When running my container with docker I need to modify one file sed -i "242s/.decode('utf-8')//" /usr/local/lib/python3.6/site-packages/keras/models.py When running the .sif file I have created from the docker image (I need this to run it on a…
Manolo Dominguez Becerra
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How to hide warning when working with apptainer

This is the code: ## The tools are images generated and excuted by apptainer export python="apptainer run /mainfs/wrgl/broadinstitute_warp_development/warp/images/datascience-notebook_latest.sif" logmessage "INFO: apptainer images were…
Manolo Dominguez Becerra
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How to run scripts in a docker image using Apptainer?

I created a docker image to run some scripts. I copy 2 Python scripts into my Docker image. The end of my Dockerfile looks like this. COPY . /app ENTRYPOINT ["python3"] When I want to run it using Docker I simply run Docker run -i image_name…
Sam H
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Apptainer pull failed to get checksum

I have access to two systems and want to run the same container on both (as far as possible). The problem is that one only supports charliecloud, the other apptainer. I found out the best way would be to push the charliecloud image to a gitlab…
Pinko
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.yml file not being read when running apptainer container

I have an apptainer .def file: Bootstrap: docker From: continuum/miniconda3 %files env.yml %post conda env create -n envname --file env.yml %runscript source activate envname python3 pythonScript.py It builds successfully, but…
Scott Caulfield
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A docker container produce errors with Apptainer unless in writable sandbox mode

A (confidential) docker container fails on tests when run by Apptainer unless it is in the writable sandbox mode. I tried ls \ -tral I see only /etc, /tmp, mounted and special folders like /.singularity.d being modified in writable sandbox. Any…
Serge
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