https://github.com/bhklab/azure-aks-snakemake-merida
Scripts to configure and run the MERIDA_snakemake_pipeline on Azure Kubernetes Service
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary
Repository
Scripts to configure and run the MERIDA_snakemake_pipeline on Azure Kubernetes Service
Basic Info
- Host: GitHub
- Owner: bhklab
- Language: Shell
- Default Branch: master
- Size: 13.7 KB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Azure Kubernetes Service (AKS) Cluster for Snakemake Deployment
Repository with code to provision an AKS cluster which can be used to dynamically scale compute resources for an arbitrary Snakemake pipeline.
Requirments
Installing Miniconda
This repo uses conda to simplify dependency management and installation. To get started with setup you can install miniconda3 using the instructions available here: https://docs.conda.io/en/latest/miniconda.html.
Setting Up Your Software Environment
The first step to deploying an analysis pipeline is to install the various software packages it depends on.
All commands should be executed from the top level directory of this repository.
Python and System Dependencies
Conda can be used to install all Python and most OS system dependencies using:
conda env create --file envs/aks-snakemake.yml
This will take some time to run as it gathers and installs the correct package versions. The environment it creates should be called aks-snakemake.
If it is not automatically activated after installation please run
conda activate aks-snakemake before proceeding to the next step.
Configuration
Open the files named dot_*, fill in your values for the requested configuration variables, then rename the files as instructed in the
comments in each file.
This will ensure your specific configuration is not pushed to the GitHub.
Deployment
TODO::
References
Owner
- Name: BHKLAB
- Login: bhklab
- Kind: organization
- Location: Toronto, Ontario, Canada
- Website: http://www.pmgenomics.ca/bhklab/
- Repositories: 168
- Profile: https://github.com/bhklab
The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre
GitHub Events
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Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| ChristopherEeles | c****s@o****m | 17 |
Issues and Pull Requests
Last synced: about 1 year ago
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- Total issue authors: 0
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- Average comments per issue: 0
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- Bot pull requests: 0
Past Year
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