The Seven Bridges Knowledge Center

The Seven Bridges Platform is a simple solution for doing bioinformatics at industrial scale. But sometimes, everyone needs a little help.

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Set execution hints at tool level

Via the visual interface

  1. Go to the Apps tab of your project dashboard.
  2. Click the pencil icon corresponding to the tool you want to edit to open the Tool Editor.
  3. In the Tool Editor, click the ellipses and select Settings.
  4. Set the tool-level instance in the pop-up:
    a. Click the plus icon :heavy-plus-sign+: .
    b. Enter the name of the hint you are setting in the Requirement class field, e.g. sbg:AWSInstanceType, sbg:GoogleInstanceType, sbg:MemRequirement, sbg:CPURequirement, sbg:SaveLogs.
    c. Enter the value for the hint in the Requirement value field, e.g. c3.8xlarge.
    d. If setting up sbg:AWSInstanceType or sbg:GoogleInstanceType hints, you can add or change the value in the Attached Storage field to define the size of attached storage.
  5. Click Save.

Via the API

  • To set tool level hints via the API, include those hints in the CWL specification of the tool when adding a new app or adding a new revision of an app.
  • Tool level hints should be placed in an array named hints at the top level of the tool JSON.
  • A hint is represented by a JSON object with the following fields:
Field Description
class The name of the hint to set
value The value to assign to this hint

AWS

{
  ...
    "hints": [
      {
        "class": "sbg:AWSInstanceType",
        "value": "c4.8xlarge;ebs-gp2;2000"
      },
      {
        "class": "sbg:CPURequirement",
        "value": "2"
      },
      {
        "class": "sbg:MemRequirement",
        "value": "2048"
      }
    ],
  ...
}

In this case, the node uses the c4.8xlarge instance with 2000 GB of attached EBS storage. The value of sbg:AWSInstanceType consists of the following three parts:

  • instance type, e.g. c4.8xlarge
  • attached disk type: ebs-gp2
  • attached disk size in GB

GCP

{
  ...
    "hints": [
      {
        "class": "sbg:GoogleInstanceType",
        "value": "n1-standard-32;pd-ssd;2000"
      },
      {
        "class": "sbg:CPURequirement",
        "value": "2"
      },
      {
        "class": "sbg:MemRequirement",
        "value": "2048"
      }
    ],
  ...
}

In case of Google Cloud Platform, the node uses the n1-standard-32 instance with 2000 GB of attached EBS storage. The value of sbg:GoogleInstanceType consists of the following three parts:

  • instance type, e.g. n1-standard-32
  • attached disk type: pd-ssd
  • attached disk size in GB