Launching AIVA Portal on Seqera studio
Tarun Mamidi
29 steps
6 minutes
Seqera
Aivaportal
From Seqera Studio to AIVA: A Complete Genomic Workflow Guide
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**Introduction** [AIVA](https://chat.aivaportal.com) is an AI clinical analyst agent that helps with analyzing genetic variants through natural language conversations. This guide demonstrates how to seamlessly integrate AIVA into your Seqera Studio workflow. What You'll Learn: - Spinning up AIVA Portal instance using Seqera Studio - Uploading pre-annotated VCFs to AIVA Portal - Collaborating on variant analysis with AIVA Prerequisites: - Pre-annotated VCF from any secondary analysis pipelines (e.g. nf-core/Sarek, raredisease, etc.) - Access to Seqera Studio and compute environment - An AIVA Portal account -[chat.aivaportal.com](https://chat.aivaportal.com)
AIVA allows you to pre-annotate VCFs to bring your in-house annotations. Please use either VEP/SnpEff/BCFTools or directly from your secondary analysis pipeline of choice for analysis.
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Navigate to [https://cloud.seqera.io/](https://cloud.seqera.io/orgs/Mamidi_Health/workspaces/AIVA/launchpad) and run your favorite variant calling pipeline (Sarek, raredisease, etc) along with variant annotation.
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Click "Data Explorer" to make sure you have the annotated VCF in your bucket
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Copy the URL path for the annotated VCF file
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Click "Studios"
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Click "Add Studio"
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Click "Mount data"
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Select the bucket with your annotated VCF files
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Click "Add (1) selected item" to mount the bucket
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Click "Mount data"
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Click "Next"
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Click to change from template to AIVA prebuilt container
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Click "Prebuilt container image"
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Click "Container identifier"
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Add AIVA container - [[gcr.io/aiva-b2387/aiva-chat-seqera:latest]]
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Click "Add and start"
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Studio will spin up AIVA instance
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Click "Login"
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Click "Samples"
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Click "Upload Files"
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Click "Cloud Import"
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Paste your VCF URL here. Replace [[s3:// or gs://]] with [[/workspace/data]] since we mounted the bucket to studio instance already. For example: [[/workspace/data/your-bucket-name/sample1-annotated.vcf.gz]]
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Click "Import from Cloud" to start the import process
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Click "Jobs" to monitor upload progress
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Larger files may take a bit longer to finish processing
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Click "Browse by Samples" to find your uploaded samples
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Click "Chat" to start analyzing...
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Start analyzing based on the annotations in VCF
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Agent executes steps (fully transparent) and returns responses
Please reach out to tarun@mamidi.co.in if you encounter any trouble in this process or need help!
