manifest.json

{
  "author": "Gaylord Holder <holder@upenn.edu>",
  "cite": "Neuroimage 2012 Apr 2;60(2):1266-79.  doi: 10.1016/j.neuroimage.2012.01.098. Epub 2012 Jan 28.\n\nMeasuring longitudinal change in the hippocampal formation from in vivo high-resolution T2-weighted MRI\n\nSandhitsu R Das, Brian B Avants, John Pluta, Hongzhi Wang, Jung W Suh, Michael W Weiner, Susanne G Mueller, Paul A Yushkevich\n\nAffiliation: Penn Image Computing and Science Laboratory-PICSL, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA. sudas@seas.upenn.edu\n\nPMID: 22306801 PMCID: PMC3667607 DOI: 10.1016/j.neuroimage.2012.01.098",
  "command": "./run -v",
  "config": {
    "Scope": {
      "default": "Subject",
      "description": "Run Aloha on the specified subject, or the whole project",
      "enum": [
        "Subject",
        "Project"
      ],
      "type": "string"
    },
    "Stages": {
      "default": "VerifyAlohaInputs",
      "description": "Which stages of the pipeline to run, default is VerifyAlohaInputs",
      "enum": [
        "AlohaT1T2TaggingReport",
        "VerifyAlohaInputs",
        "RunAloha",
        "CalculateAtrophyRates",
        "VerifyAlohaInputs,RunAloha"
      ],
      "type": "string"
    },
    "MachineSize": {
      "default": "extra-large",
      "description": "May be extra-large, 8 vCPUs, or supersize, 32 vCPUs",
      "enum": [
        "none",
        "extra-large",
        "supersize"
      ],
      "type": "string"
    }
  },
  "description": "Aloha Gear",
  "environment": {
    "PATH": "/flywheel/v0/flywheel/bin:/tk/greedy/build:/tk/cmrep/build:/tk/c3d/build:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/scripts:/aloha/ext/Linux/bin",
    "LD_LIBRARY_PATH": "/tk/vtk/build/lib",
    "FLYWHEEL": "/flywheel/v0",
    "ALOHA_ROOT": "/flywheel/v0/aloha",
    "PYTHONPATH": "/flywheel/v0/flywheel/lib",
    "PWD": "/flywheel/v0"
  },
  "custom": {
    "gear-builder": {
      "image": "aloha:0.1.30",
      "category": "analysis"
    },
    "flywheel": {
      "show-job": true,
      "suite": "BrainScienceCenter"
    }
  },
  "inputs": {
    "input-file": {
      "base": "file",
      "optional": false,
      "description": "Input file for the gear"
    },
    "api-key": {
      "base": "api-key",
      "read-only": false
    }
  },
  "label": "Aloha",
  "name": "aloha",
  "source": "",
  "url": "",
  "license": "MIT",
  "version": "0.1.30"
}