Get raw CWL for an app revision

This call returns information about the specified app revision, as raw CWL. The call differs from the call to get the details of an app revision by returning a JSON object that is the CWL description of the app revision.

The app should be one in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.

https://api.sbgenomics.com/v2/apps/{app_id}/raw
https://eu-api.sbgenomics.com/v2/apps/{app_id}/raw

👍

app_ids

Recall from the apps section in the API overview that the app-id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.

You can get the app-id for an app by making the call to list all apps available to you

Request

Example request

GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl  -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"
from sevenbridges import Api

api = Api(url='https://api.sbgenomics.com/v2',
          token='3259c50e1ac5426ea8f1273259740f74')

# send GET request to SB API
app = api.apps.get(id='RFranklin/my-project/bamtools-merge-2-4-0/0')

print(app.raw)

Header Fields

Name

Description

X-SBG-Auth-Token
required

Your Seven Bridges Platform authentication token.

Path parameters

Name

Description

app_id

The ID for the app you are querying. It can be obtained by making the call to list all apps available to you

revision number

The integer that is the revision number of the app

Query parameters

Name

Data type

Description

fields

string

Selector specifying a subset of fields to include in the response.

Response

See a list of Seven Bridges Platform-specific response codes that may be contained in the body of the response.

Example response body

Note that this call returns the full CWL description of the app.

{
  "successCodes": [],
  "sbg:homepage": "https://github.com/pezmaster31/bamtools/wiki",
  "sbg:validationErrors": [],
  "sbg:sbgMaintained": false,
  "temporaryFailCodes": [],
  "requirements": [],
  "sbg:latestRevision": 0,
  "description": "BamTools Merge merges multiple BAM files into a single file.",
  "sbg:job": {
    "inputs": {
      "region": "chr1",
      "input_bam_files": [
        {
          "path": "1.bam"
        },
        {
          "path": "2.bam"
        }
      ]
    },
    "allocatedResources": {
      "cpu": 1,
      "mem": 1000
    }
  },
  "sbg:toolAuthor": "Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg",
  "hints": [
    {
      "dockerImageId": "f808163d4cd3",
      "class": "DockerRequirement",
      "dockerPull": "images.sbgenomics.com/markop/bamtools:2.4.0"
    },
    {
      "value": 1,
      "class": "sbg:CPURequirement"
    },
    {
      "value": 1000,
      "class": "sbg:MemRequirement"
    }
  ],
  "sbg:copyOf": "djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0",
  "sbg:createdOn": 1452181866,
  "arguments": [
    {
      "position": 1,
      "prefix": "-out",
      "separate": true,
      "valueFrom": "merged.bam"
    }
  ],
  "outputs": [
    {
      "sbg:fileTypes": "BAM",
      "id": "#output_bam_file",
      "outputBinding": {
        "glob": "merged.bam",
        "sbg:metadata": {},
        "sbg:inheritMetadataFrom": "#input_bams"
      },
      "description": "Output BAM file.",
      "type": [
        "File"
      ],
      "label": "Output BAM file"
    }
  ],
  "sbg:categories": [
    "SAM/BAM-Processing"
  ],
  "sbg:contributors": [
    "RFranklin"
  ],
  "sbg:links": [
    {
      "id": "https://github.com/pezmaster31/bamtools",
      "label": "Homepage"
    },
    {
      "id": "https://github.com/pezmaster31/bamtools/wiki",
      "label": "Wiki"
    }
  ],
  "stdout": "",
  "stdin": "",
  "sbg:project": "RFranklin/my-project",
  "inputs": [
    {
      "sbg:fileTypes": "BAM",
      "id": "#input_bam_files",
      "inputBinding": {
        "sbg:cmdInclude": true,
        "prefix": "-in",
        "separate": true,
        "itemSeparator": null,
        "position": 0
      },
      "description": "The input BAM files.",
      "label": "Input BAM files",
      "type": [
        {
          "type": "array",
          "items": "File"
        }
      ],
      "sbg:category": "Input & Output"
    },
    {
      "id": "#region",
      "inputBinding": {
        "sbg:cmdInclude": true,
        "position": 2,
        "separate": true,
        "prefix": "-region"
      },
      "description": "A region of interest (e.g. \"chr1:500..chr3:1500\"). See the documentation for more info.",
      "label": "Region of interest",
      "type": [
        "null",
        "string"
      ],
      "sbg:category": "Input & Output"
    }
  ],
  "label": "BamTools Merge",
  "sbg:createdBy": "RFranklin",
  "baseCommand": [
    "/opt/bamtools/bin/bamtools",
    "merge"
  ],
  "sbg:toolkitVersion": "2.4.0",
  "sbg:id": "RFranklin/my-project/bamtools-merge-2-4-0/0",
  "sbg:license": "The MIT License",
  "sbg:revision": 0,
  "sbg:cmdPreview": "/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1",
  "sbg:modifiedOn": 1452181866,
  "id": "https://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/",
  "class": "CommandLineTool",
  "sbg:modifiedBy": "RFranklin",
  "sbg:revisionsInfo": [
    {
      "sbg:modifiedBy": "RFranklin",
      "sbg:modifiedOn": 1452181866,
      "sbg:revision": 0
    }
  ],
  "sbg:toolkit": "BamTools"
}