AnVIL Docker Image for OCHA book
This Dockerfile is to load a custom environment in AnVIL terra to run the ohca analysis: ghcr.io/linkmonica/ocha4anvil:latest This will install all required packages and example datasets used throughout the chapters.
After loading the custom environment using the above image, it should be possible to select a book chapter and run the required analysis, without any installations.
Analysis is divided into 4 main parts: Memory and CPUs/cores required to run each chapter or part are mentioned below.
- Hi-C pre-processing steps: 4 cores, 26GB memory
- Hi-C data structures in R: 2 cores, 7.5GB memory
- Manipulating Hi-C data in R: 2 cores, 7.5GB memory
- Hi-C data visualization: 2 cores, 7.5GB memory
- Matrix-centric analysis: 4 cores, 26GB memory
- Interactions-centric analysis: 2 cores, 7.5GB memory
- Finding topological features in Hi-C: 2 cores, 7.5GB memory
- Data gateways: 4 cores, 26GB memory
- Interoperability: 2 cores, 7.5GB memory
- Workflow1: Distance-dependent interactions across yeast mutants
- Workflow2: Chromosome compartment cohesion upon mitosis entry
- Workflow3: Inter-centromere interactions in yeast