Questions tagged [singularity-container]

For questions about programmatic problems relating to the Singularity scientific computing container solution.

Singularity is a container solution created by necessity for scientific and application driven workloads. Singularity provides four primary functions (taken from the preceding link):

  1. Mobility of compute: the ability to define, create and maintain a workflow and be confident that the workflow can be executed on different hosts, operating systems (as long as it is Linux) and service providers.
  2. Reproducibility: once a contained workflow has been defined, the container image can be snapshotted, archived, and locked down such that it can be used later and you can be confident that the code within the container has not changed.
  3. User freedom: users can define their own working environment and literally copy that environment image (single file) to a shared resource, and run their workflow inside that image.
  4. Support on existing traditional HPC: Singularity supports existing and traditional HPC resources as easily as installing a single package onto the host operating system. Custom configurations may be achieved via a single configuration file, and the defaults are tuned to be generally applicable for shared environments.
365 questions
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bash script to perform action in a singularity container it opens

I am using the following workflow on RedHat in terminal: open a singularity image: singularity run /mn/sarpanitu/singularity/test/fenics-and-more.img export some display inside the singularity: export DISPLAY=:0.0 export a path to gmsh inside…
Zorglub29
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Building Singularity recipe from Nipype docker image CommandNotFound

I have the following Singularity container recipe: #!/bin/bash Bootstrap: docker From: nipype/nipype:latest %labels Version v1.0 %post # Install nano apt-get update apt-get install nano # Set up Python environment …
user9761559
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Python script file missing in Singularity image

In AWS, created a docker image with a python script to print a string(basicprint.py) docker file: FROM python COPY ./basicprint.py ./ CMD ["python", "basicprint.py"] It works fine then saved docker image as .tgz file. copy that .tgz file in to my…
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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…
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Using Docker with Snakemake (as motivated by the Snakemake documentation) does not provide a true docker container?

In order to improve the distribution of my snakemake workflow, I am wanting to Docker-ize it. The way I usually deploy my software stack is through conda environments (saved as .yaml files within an envs/ directory of my project folder). They are…
epigenome
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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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Error pulling docker image with singularity from gitlab container registry

I am trying to pull a docker image from my Gitlab container registry using singularity pull (as I want to use it singularity), but I get an error from singularity telling me that one file is not a tar archive. Indeed this file contains
stackoverflowed
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Singularity container with stringr fails only locally with 'libicui18n.so.66: cannot open shared object file: No such file or directory'

I enjoy using the Singularity container software, as well as the R package 'stringr' to work with strings. What I fail to understand is why a Singularity container fails locally (i.e. on my Ubuntu 20.04 computer), yet passes remotely (i.e. on GitHub…
richelbilderbeek
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Using the R package reticulate within a Singularity container

reticulate is an R package to call Python code from R, that I find easy to use on my local computer and I sometimes get working within a Singularity container. In this question I will post a simple reprex about code that worked two months ago, at…
richelbilderbeek
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Is Nextflow really inconsistent or am I doing something wrong using nf-core/rnaseq?

I want to preface this with I am very new to Nextflow, and if I don't include a key to debugging I am sorry please just let me know. ==================================== Case 1: I tried to run this command: nextflow run nf-core/rnaseq --aligner…
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singularity run or execute command as the same as docker run

I am working under a university's HPC system, which has only singularity installed and without docker. I want to run an already singularity-pulled docker image (julia_adfem_v1.sif). The original command for the docker environment is docker run -ti…
Riter E
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Is it possible to create a Singularity image from Dockerfile?

I have Singularity installed. In my repo I have Dockerfile. I want to create a SIF (Singularity Image) from that Dockerfile. I tried to look the docs and check the docker build option but it does not contain an option for Dockerfile. Is it possible…
vesii
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Unable to build writable singularity container

I am trying to build a writable singularity container with the command sudo singularity build --writable my_container.img docker://image_name, but I get the error Error for command "build": unknown flag: --writable. I decided to follow a guide from…
Josh Loecker
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Can I create a Singularity container which others cannot run with root privileges?

I am not very experienced with the finer details of Singularity containers yet and I was wondering if an admin on a system can create Singularity containers which they can let ordinary users run, but preventing them from running with root…
Thomas Arildsen
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