getdemo / README.md
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metadata
title: GET
app_file: app/main.py
colorFrom: gray
colorTo: red
sdk: docker
license: cc-by-nc-4.0
pinned: false

Data preparation

Put the data in the following structure in the root directory of the project.

data
β”œβ”€β”€ sequences
β”‚   └── causal
β”‚       β”œβ”€β”€ MECP2_TFAP2A
β”‚       β”œβ”€β”€ PRDM1_SMAD2
β”‚       └── TAF1_ZFX
└── structures
    β”œβ”€β”€ causal
    β”‚   β”œβ”€β”€ MECP2_TFAP2A
    β”‚   β”œβ”€β”€ PRDM1_SMAD2
    β”‚   └── TAF1_ZFX
    └── homodimer
        β”œβ”€β”€ PRDM1
        β”œβ”€β”€ SMAD2
        β”œβ”€β”€ TAF1
        └── ZFX

Installation

git clone --recursive [email protected]:fuxialexander/getdemo.git
cd getdemo
docker pull fuxialexander/getdemo:latest
docker run -it -v "/path/to/data:/data" --rm -p 7860:7860 fuxialexander/getdemo
# or
singularity run  -w --bind /manitou/pmg/users/xf2217/getdemo:/app --bind /manitou/pmg/users/xf2217/demo_data:/data --bind /pmglocal/xf2217/tmp:/tmp --no-home --pwd /app getdemo

The gradio interface will be available at http://127.0.0.1:7860, a sharable link will be printed in the terminal.

Build

git clone --recursive [email protected]:fuxialexander/getdemo.git
cd getdemo
docker build -t getdemo .
docker run -it -v "/path/to/data:/data" --rm -p 7860:7860 getdemo