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Hi, great work with the pipeline.
Unfortunately, my university does not allow docker on the HPC, but they will whitelist and install Singularity/Apptainer images on request.
Can I just point the…
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DL benchmarks could also get executed within HPC environments.
Often singularity is the container engine used within HPC therefore singularity should be supported.
https://sylabs.io/singularity/
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Singularity is available on all compute nodes via
`module load singularity/2.6.0`
https://rcstatus.asu.edu/agave/howto/software_modules.php
From William Dixon:
> Also take note, you'll nee…
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## Issue description
I intend to start using nixpkgs' `singularity-tools` for hpc applications.
What follows is a list of hindrances and minor annoyances that I've immediately encountered.
The li…
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Hi there,
I've been trying to use TransPi (love the concept and the benchmarking in the paper looks great!) to re-assemble some older public datasets. Running on an interactive slurm session of an …
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### 1. Lesson Topic
Introduction to Apptainer
### 2. Lesson Language
English
### 3. Draft materials
https://unlhcc.github.io/apptainer-introduction/
### 4. Requirements for existing materials
-…
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### Description of the bug
Hello, I am a newbie to nf-core sarek and I am running it on WES data for tumor-only, using CNVkit tool. Even though the pipeline completes successfully, the CNVkit tool …
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Hi, Sorry for bothering you again! First, thanks!
I'm slowly pushing forward in running your pipeline, and have encountered the issues below:
1, as posted, the pipeline failed to install IEDB, due…
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### Description of the bug
Hi,
I am running 40 samples on Sarek pipeline. A little number of samples are producing an error
during the FASTP stage but other samples run completely the pipeline.
Al…
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Hi, we are learning from this project. Because our HPC does not give us the root authority to use Docker, we have to either build a Singularity image based on a Docker image, or build the Docker image…