DNAnexus App for checking md5

dxapp.json

{
  "name": "md5check",
  "title": "MD5 checksum",
  "summary": "Generate MD5 checksum of one or more files and save the output info in a text file. Hard timeout policy for 10hrs.Use batch input processing or instance of large storage if you have large amount of data to process. Questions go to [email protected]",
  "dxapi": "1.0.0",
  "version": "0.0.1",
  "inputSpec": [
    {
      "name": "i_put",
      "label": "Input File(s)",
      "class": "array:file",
      "optional": false,
      "patterns": [
        "*"
      ],
      "help": ""
    }
  ],
  "outputSpec": [
    {
      "name": "md5_output",
      "label": "Output File",
      "class": "file",
      "patterns": [
        "*"
      ],
      "help": ""
    }
  ],
  "runSpec": {
    "timeoutPolicy": {
      "*": {
        "minutes": 600
      }
    },
    "interpreter": "bash",
    "release": "16.04",
    "distribution": "Ubuntu",
    "file": "src/md5check.sh"
  },
  "access": {"network": ["*"], "project": "CONTRIBUTE", "allProjects": "VIEW"},
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem1_ssd1_v2_x8"
        }
      }
    }
  }
}

md5check.sh

#!/bin/bash
# md5check 0.0.1
# Generated by dx-app-wizard.
# Questions go to [email protected]

set +e -x -o pipefail

main() {
    echo "Value of i_put: '${i_put[@]}'"
    for i in ${!i_put[@]}
    do
        filename=`dx describe --name "${i_put[$i]}"`
        dx download "${i_put[$i]}" -o $filename
        md5sum $filename >> md5_output.txt
    done
    o_put=$(dx upload md5_output.txt --brief)
    dx-jobutil-add-output "md5_output" "$o_put" --class=file
}