APGAP Quickstart Guide#

Welcome to APGAP! This guide will get you up and running in minutes, regardless of your role. If you run into anything that isn’t covered here, reach out to your Lab Director or Platform Admin.

Before You Begin#

You’ll need: An institutional email address from an approved domain (ASU, ADHS, University of Arizona, Northern Arizona University, TGen, or a partner organization) An account created by a Platform Admin — APGAP does not support self-signup Access to at least one Lab, assigned by your Lab Director or Platform Admin If you don’t have an account yet, contact your Lab Director or your organization’s Platform Admin and provide your institutional email address.

Step 1 — Log In#

Open a browser and navigate to https://apgap.prod.rtd.asu.edu Click Sign in with Google Select your institutional Google account — this must match the email address registered in APGAP After a moment you’ll be redirected to your dashboard Trouble logging in?

Step 2 — Find Your Way Around#

After logging in you’ll land on the Dashboard. The left sidebar is your main navigation: Labs — your labs and their sequences, projects, and rosters Data Catalog — browsable view of datasets available for analysis Notifications — the bell icon shows requests, approvals, and system messages Admin — visible to Platform Admins only Your role determines what you see and can do. Here’s a quick summary: Role What you can do **Lab Collaborator Upload sequences, add metadata, view and download files in your lab **Lab Reader View and download files in your lab; no upload or edit access Lab Director Everything a Collaborator can do, plus manage lab membership, approve access requests, and manage projects Bioinformatics User Access specific projects, launch pipelines, work with analytical datasets Data Analyst Platform-wide read access to datasets; cannot be assigned to individual labs Platform Admin Full access to all organizations, labs, users, and settings

Step 3 — Your First Task (by Role)#

If you’re a Lab Director#

Start by making sure your lab is fully set up. Click Labs → your lab and check:

• Lab Roster — are all your team members added with the right roles?
• Sequences — are there any files in DRAFT status that need attention?
• Projects — are the right Bioinformatics Users assigned? To add a team member to your lab:

1. Click Labs → your lab → Lab Roster
2. Click Assign User
3. Search for the user by email address
4. Select their role and click Assign User If the user isn’t found, they haven’t been created in the system yet — ask your Platform Admin to create the account first.

If you’re a Bioinformatics User#

Your access is project-based. Click Labs in the sidebar and navigate to the lab that contains your project. Within the lab, click the Projects tab, then select your project.

From your project you can:

• Browse and download files in your project
• Create and manage Analytical Datasets
• Launch pipelines through the Seqera integration (if your project workspace has been provisioned) To get started with an Analytical Dataset:

1. Navigate to your Project
2. Click Datasets → New Dataset
3. Give it a name, add files, and save If the Pipelines section of your project is empty, the Seqera workspace may not have been set up yet — contact your Platform Admin.

If you’re a Lab Collaborator or Lab Reader#

Your primary home is your Lab. Click Labs in the sidebar, then click your lab name. You’ll see tabs for Sequences, Projects, Lab Roster, and Batch Endpoints.

To upload your first sequence file:

1. Click Labs → select your lab
2. Click the Sequences tab
3. Click Upload Sequences → GUI Upload
4. Drag and drop your file, or click to browse
5. Click Upload Files Your file will move through PROCESSING → UPLOADED or DRAFT within about a minute. If it lands in DRAFT, it needs metadata before it can be used in analysis — see the How-To Guide for instructions.

If you’re a Platform Admin#

Your first actions after a fresh deployment should be:

1. Add your organization’s email domain → Admin → Domain Whitelist → New Domain
2. Create your organization → Admin → Organizations → Add New Organization
3. Create user accounts → Admin → User Management → Add User
4. Create labs → Labs → Create Lab (this triggers a 5–15 minute provisioning process)
5. Assign users to labs via User Management or from the Lab Roster tab

The full Admin Guide covers each of these in detail, including recovery procedures for failed lab provisioning.

Understanding File Statuses#

Every file in APGAP has a status. Here’s what they mean:

The most common status to pay attention to is DRAFT. A file in DRAFT has been successfully stored in the platform — it isn’t lost — but it needs complete metadata before it can be used in analysis or shared with other researchers.

Sequera#

APGAP uses Seqera Platform (formerly Nextflow Tower) to run bioinformatics pipelines. Each APGAP project gets its own dedicated Seqera workspace, which is provisioned automatically when the project is created — this is why creating a project triggers a few-minute background job before pipelines become available.

About Seqera#

APGAP integrates with Seqera Platform (formerly Nextflow Tower) to handle the actual execution of bioinformatics pipelines. Seqera is built by the creators of Nextflow — the open-source workflow language widely used in genomics — and it provides the orchestration, monitoring, and compute management that running pipelines at scale requires. Rather than reinventing this in APGAP, the platform launches pipelines through Seqera and tracks results back into your project.

Each APGAP project maps to a dedicated Seqera workspace that gets provisioned automatically when you create the project. Inside that workspace, the Launchpad is your catalog of pre-configured pipelines (typically nf-core pipelines or custom workflows) ready to run against your data.

Note: Provisioning a workspace takes a few minutes after project creation. If the Pipelines section stays empty for more than 10–15 minutes, the workspace likely failed to provision — contact your Platform Admin.

Getting Help#

• Lab-level questions (access, file issues, metadata): contact your Lab Director
• Account or domain issues: contact your Platform Admin
• Technical platform issues: contact the APGAP support team through your organization’s helpdesk channel