SciApps Guide¶
Goal¶
Introduce SciApps, a cloud-based platform for building and sharing reproducible bioinformatics workflows across distributed computing and storage systems. This guide will cover accessing CyVerse Data Store, launching analysis jobs, visualizing results, building, sharing, and running workflows.
- Platform guide home
- SciApps Basics and Logging In
- Viewing and Accessing Data
- Launching an Analysis Job
- Building a Workflow
- The Annotation Tutorial
- The Association Tutorial
- The BSA Tutorial
- Step 1: Requiring access to SciApps
- Step 2: Uploading data for SciApps
- Step 3: Variant filtering with bcftools_filter
- Step 4: Annotating variant with SnpEff
- Step 5: Predicting variant effects with SIFT
- Step 6: Visualizing EMS outputs
- Step 7: Finding mutant lines with significant mutation on the same candidate gene
- Step 8: Finding mutant lines with significant mutation on the same candidate gene using Ensembl Plants/Gramene (Optional)
- Summary
- The MaizeCODE Tutorial
Prerequisites¶
Downloads, access, and services¶
In order to complete this tutorial, you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | Register |
| SciApps access | You will need to request access to SciApps from the user portal. Check the ‘My Services’ tab; if SciApps is not listed, click the ‘Available’ tab, locate SciApps and click the link to request access. | CyVerse User Portal |
Fix or improve this documentation
- Search for an answer: |CyVerse Learning Center|
- Ask us for help: click |Intercom| on the lower right-hand side of the page
- Report an issue or submit a change: |Github Repo Link|
- Send feedback: Tutorials@CyVerse.org