https://github.com/audy/snakemake-hello-world

(demo) Minimal working map-reduce pattern in Snakemake (with containerization)
https://github.com/audy/snakemake-hello-world

Last synced: 20 days ago
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(demo) Minimal working map-reduce pattern in Snakemake (with containerization)

• Host: GitHub
• URL: https://github.com/audy/snakemake-hello-world
• Owner: audy
• Created: 2024-06-05T22:11:22.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2024-06-06T15:31:08.000Z (6 months ago)
• Last Synced: 2024-10-23T02:29:10.831Z (28 days ago)
• Language: Python
• Homepage:
• Size: 1000 Bytes
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# snakemake-hello-world

Minimal working map-reduce pattern in Snakemake (with containerization)

## Instructions

You'll need to install Singularity + LIMA + QEMU to run the pipeline with

containers inside of a VM.

- Install Apptainer (nee Singularity) by following [these

  instructions](https://apptainer.org/docs/admin/main/installation.html#installation-on-windows-or-mac)

- From this repo, `limactl shell apptainer`

- (In VM) Copy this directory to `~` inside of VM so you can write to it

- (In VM) `sudo apt-get install -y python3 python3-pip && pip3 install snakemake setuptools`

- (In VM) `snakemake -j 1 --use-singularity`