I’m starting to experiment with using containers with Snakemake, and I have a question about what needs to be pre-build into the container and what doesn’t. For example: I want to run a python script (stored in workflow_root/scripts/myScript.py, for example) in a container with a pipe in from another program. Do I need to build ..
Category : singularity-container
I’m trying to launch a singularity container on a hpc cluster. I have been running the projectNetv2.sif and sandbox on my local with no issue. After exporting them to a hpc I get the following error. (singularity) [[email protected] Project]$ ls examples projectnet_image_v2.tar.gz projectnet_sandboxv2 projectNetv2.sif (singularity) [[email protected] Project]$ singularity run projectNetv2.sif INFO: Converting SIF file to ..
I have looked hard for an answer, but haven’t managed to find one, so I’m hoping someone here can help me understand this error and what is happening during the singularity pull command. Here is the error: Error executing process > ‘QC_TRIM_READS (1)’ Caused by: Failed to pull singularity image command: singularity pull –name quay.io-biocontainers-sickle-trim-1.33–2.img.pulling.1632264509884 ..
I am trying to convert a Docker image to a Squashfs image. However, a lot of No space left on device errors occurred while building. $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/test:/output –privileged -t –rm quay.io/singularity/docker2singularity container:latest Image Format: squashfs Docker Image: container:latest Inspected Size: 20424 MB (1/10) Creating a build sandbox… (2/10) Exporting filesystem… ..
I am trying to convert a Docker image to a Squashfs image following this instruction. https://github.com/singularityhub/docker2singularity#build-a-squashfs-image However, a lot of No space left on device errors occurred while building. How can I solve this? $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/test:/output –privileged -t –rm quay.io/singularity/docker2singularity container:latest Image Format: squashfs Docker Image: container:latest Inspected Size: 20424 ..
I am trying to convert a Docker image to a Squashfs image following this instruction. https://github.com/singularityhub/docker2singularity#build-a-squashfs-image However, a lot of No space left on device errors occurred while building. How can I solve this? $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/test:/output –privileged -t –rm quay.io/singularity/docker2singularity container:latest Image Format: squashfs Docker Image: container:latest Inspected Size: 20424 ..
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 histat2 -profile test,docker But ended up getting this error: -[nf-core/rnaseq] Pipeline completed with ..
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 histat2 -profile test,docker But ended up getting this error: -[nf-core/rnaseq] Pipeline completed with ..
Is there a singularity equivalent to docker image list? The Singularity 3.8 documentation states that All cache entries are named using a content hash which makes sense when checking for identical layers/images, but has no semantic meaning whatsoever. Compare this to docker’s docker image list which lists the images that you already have with semantically ..
My company is going to replace Docker to Singularity as the container solution. What should I be aware before this migration? Thanks, Chance Source: Docker..
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