dxapp.json

{
  "inputSpec": [
    {
      "name": "BAM",
      "label": "Bam File",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.bam"
      ]
    },
    {
      "name": "BAM_INDEX",
      "label": "Bam File Index",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.bai"
      ]
    },
    {
      "class": "string",
      "label": "Genome",
      "name": "ref_name",
      "optional": false,
      "choices": ["GRCh37-lite", "GRCh38_no_alt"],
      "default": "GRCh37-lite",
      "help": "" 
    }
  ],
  "categories": [],
  "version": "COVERAGE_SHORT_VERSION",
  "dxapi": "1.0.0",
  "details": {
    "contactEmail": "clay.mcleod@stjude.org"
  },
  "summary": "Build a BigWig file from a BAM",
  "title": "Coverage BW (St. Jude)",
  "openSource": true,
  "developers": [
    "user-clmcleod",
    "user-athrashe"
  ],
  "authorizedUsers": [
    "user-clmcleod",
    "user-snewman",
    "user-appdpdnanexus_stjude.org",
    "user-appdddnanexus_stjude.org",
    "org-stjude_cloud_app_runners",
    "org-stjude_cloud"
  ],
  "regionalOptions": {
    "azure:westus": {
      "systemRequirements": {
        "*": {
          "instanceType": "azure:mem3_ssd1_x2"
        }
      }
    },
    "aws:us-east-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem3_ssd1_x2"
        }
      }
    }
  },
  "billTo": "org-stjude_cloud",
  "runSpec": {
    "interpreter": "bash",
    "file": "src/coverage_bw.sh",
    "execDepends": [
      {
        "name": "openjdk-11-jre-headless"
      },
      {
        "name": "samtools"
      },
      {
        "name": "libssl1.1"
     },
     {
        "name": "libssl-dev"
     },
     {
        "name": "libmysqlclient-dev"
     }
    ],
    "distribution": "Ubuntu",
    "release": "20.04",
    "version": "0"
  },
  "outputSpec": [
    {
      "name": "coverage_bw",
      "label": "Coverage File",
      "class": "file"
    }
  ],
  "name": "stjude_coverage_bw",
  "access": {
    "allProjects": "VIEW"
  }
}