manifest.json

{
  "name": "deepliif-predict",
  "label": "DeepLIIF - IHC prediction",
  "description": "This package provides IHC prediction using the DeepLIIF algorithm.",
  "author": "D3b-TIRU",
  "maintainer": "D3b-TIRU <flywheel@d3b.center>",
  "url": "https://github.com/nadeemlab/DeepLIIF/tree/main",
  "source": "https://github.com/d3b-center/deepliif-predict", 
  "version": "0.0.1-1",
  "license": "Apache-2.0",
  "custom": {
    "gear-builder": {
      "category": "analysis",
      "image": "chop.flywheel.io/deepliif-predict:0.0.1-1"
    },
    "flywheel": {
      "suite": "DeepLIIF"
    }
  },
  "inputs": {
    "image": {
      "base": "file",
      "description": "Digital slide image",
      "optional": false
    }
  },
  "config": {
    "tile_size": {
      "description": "Tile size (default: 512).",
      "type": "integer",
      "default":512
    },
    "wsi": {
      "description": "Whether WSI image or not (default: true).",
      "type": "boolean",
      "default":true
    },
    "region_size": {
      "description": "Region size for WSI files (default: 20000).",
      "type": "integer",
      "default":20000
    },
    "output_results_pickle": {
      "description": "Whether to output the results.pkl file (default: False).",
      "type": "boolean",
      "default":false
    }
  },
  "environment":{
    "HOME":"/root",
    "HOSTNAME":"0b633f948575",
    "MESA_GL_VERSION_OVERRIDE":"3.2",
    "PATH":"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
    "QT_GRAPHICSSYSTEM":"native",
    "QT_X11_NO_MITSHM":"1",
    "SHLVL":"1",
    "TERM":"xterm"
  }
}