build an automated workflow visual workflow creator discovery environment
TRANSCRIPT
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.
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
Log in to Discovery Environment
iPlant Discovery Environment
Add Apps to workflow
Demo workflow – align sequences and build ML tree
1. Click on Apps
2. Click Create and select Workflow
iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree
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
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
iPlant Discovery Environment
Launch workflow
Demo workflow – align sequences and build ML tree
iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree
10. Click on Apps
11. Launch your workflow (Apps ‘Workspace’ section)
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
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
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
iPlant Discovery Environment
Monitor the job progress and view results
Demo workflow – align sequences and build ML tree
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
iPlant Discovery EnvironmentDemo workflow – align sequences and build ML tree
Sample output from MUSCLE – RAxML workflow
Need more help?ask.iplantcollaborative.org
The iPlant Collaborative is funded by a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).