Functional Genomics Center Zurich

Sushi Documentation — Basic Usage

Contents

  1. Login
  2. Main Menu
  3. Import DataSet
  4. Run Sushi Application
  5. Check Job Status
  6. Check Result

1. Login
  • Please use your B-Fabric account (ID and Password)
  • If you do not have an account, please register in B-Fabric system first

2. Main Menu
  • You can see main menu below after you succeed in logging-in Sushi
  • DataSet: You can see, edit and delete DataSet.
  • Import DataSet: You can import a DataSet from .tsv file.
  • Check Jobs: You can check your submitted jobs and the status.
  • gStore: You can browse reslut files.
top right
  • Sign out: Logout from Sushi
  • Today's Menu: Go back to the top menu
  • SushiApp List: All available Sushi Applications will be shown
  • Help: Sushi Documentation
  • Project: You can select your project from the drop-down list, and 'GO' button switches to the project page

3. Import DataSet
  • You can import a DataSet file (.tsv) in Sushi database.
  • DataSet Name can be set.
  • If you want to make a relation to an existing DataSet, you can put the DataSet ID in 'Parent DataSet ID' box.

4. Run Sushi Application
  • Clicking and DataSet from top menu and selecting one DataSet, then you can see samples in the DataSet and application buttons available will be shown.
  • If there is no application available for the DataSet, no button will be shown.
  • After clicking an application button, parameter setting view will come.
  • It is an esample of FastQC application view below.

Parameters

  • Name: This will be a part of result folder name
  • Comment: You can add some comment
  • Cores: Number of cores for parallel calculation
  • RAM: Expected memory amount to be used
  • Scratch: Expected working disk space to be used
  • Node: Cluster node on which the job will run
  • Process Mode: Sample mode or DataSet mode (Usually it is fixed)
  • cmdOption: specific command like option (depending on application)
Note
  • The other parameter(s) are defined depending on the Sushi application

5. Check Job Status
  • 'Check Jobs' menu shows submitted job statuses
  • The job status becomes running, fail, or success

6. Check Result
  • If a job sceeds and finish, a new DataSet is generated.
  • If the output DataSet has a column with Link tag (e.g. FastQC see below), you can see the more detail by clicking the link.