18
Build an Automated Workflow Visual Workflow Creator Discovery Environment

Build an Automated Workflow Visual Workflow Creator Discovery Environment

Embed Size (px)

Citation preview

Page 1: Build an Automated Workflow Visual Workflow Creator Discovery Environment

Build an Automated Workflow

Visual Workflow Creator

Discovery Environment

Page 2: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Add Apps to workflow

Launch workflow

Monitor the job progress and view results

Task: Create a workflow that will build a multiple alignment of sequences from a FASTA file and then compute a maximum likelihood phylogenetic tree.

Page 3: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Tip: Not every App can be integrated into a workflow, some limitations:

• Currently only linear workflows may be created.

• Apps to be used must have inputs and outputs that have been described in metadata by the App’s integrator. In some cases you may edit the App to make it compatible.

• If an App prepends part of the input filename onto the output filename, currently the App cannot be included in a workflow

Page 4: Build an Automated Workflow Visual Workflow Creator Discovery Environment

Log in to Discovery Environment

Page 5: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery Environment

Add Apps to workflow

Demo workflow – align sequences and build ML tree

Page 6: Build an Automated Workflow Visual Workflow Creator Discovery Environment

1. Click on Apps

2. Click Create and select Workflow

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Page 7: Build an Automated Workflow Visual Workflow Creator Discovery Environment

3. On the Automate Workflow window click Switch View

4. Edit the workflow name and description

5. Search for MUSCLE 3.8.31 and drag the App into the workflow builder

6. Search for RAxML-7.3.0 and drag the app into the workflow builder

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Page 8: Build an Automated Workflow Visual Workflow Creator Discovery Environment

7. Expand the outputs of Muscle-3.8.31 App

8. Drag the phylip_interleaved.aln output into the input option of RAxML-7.3.0

9. Click Save

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Page 9: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery Environment

Launch workflow

Demo workflow – align sequences and build ML tree

Page 10: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

10. Click on Apps

11. Launch your workflow (Apps ‘Workspace’ section)

Page 11: Build an Automated Workflow Visual Workflow Creator Discovery Environment

If desired:

• Enter a name/description for the analysis

• Choose an alternative output folder for the analysis

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Page 12: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

12. Click on Muscle-3.8.31 -Select input data

13. For ‘Select Multiple Sequence File (FASTA format)’ Click Browse and locate the input file:

Community Data > iplant_training > intro_phylogenetics > 01_input_data >atpB.fa

Page 13: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

14. Click on RAxML-7.3.0 –Sequence type

15. Select DNA

16. Click on RAxML-7.3.0 Select input data

17. For ‘Sequence Type’ select DNA; click Launch Analysis

Page 14: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery Environment

Monitor the job progress and view results

Demo workflow – align sequences and build ML tree

Page 15: Build an Automated Workflow Visual Workflow Creator Discovery Environment

18. Click on Analyses

19. Monitor job until status is ‘Completed’

20. Click on the job name to view the result of the job

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Page 16: Build an Automated Workflow Visual Workflow Creator Discovery Environment

iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree

Sample output from MUSCLE – RAxML workflow

Page 17: Build an Automated Workflow Visual Workflow Creator Discovery Environment

Need more help?ask.iplantcollaborative.org

Page 18: Build an Automated Workflow Visual Workflow Creator Discovery Environment

The iPlant Collaborative is funded by a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).