Admin Quickstart

Review bootstrap accounts

Log in with the administrator account created by the guided installer. If an unattended install used the published default accounts (admin@example.com / admin and user@example.com / user), change or remove them immediately.

Set up site information

Navigate to Admin → Settings and configure:

• Site Name — your facility’s display name
• Primary/Secondary Colors — branding colors
• Contact Email — shown to researchers for support
• Logo and Favicon — optional branding assets

Create departments

Go to Admin → Departments and add your research departments. Departments organize researchers and can optionally enable department-level sequencing order sharing (configured in Settings → Extra Settings).

Configure sequencing technologies

Under Admin → Sequencing Technology, review and configure:

• Platforms — Illumina, Oxford Nanopore, PacBio, etc.
• Instruments — specific models per platform
• Library Kits — available library preparation kits

Enable or disable technologies as needed for your facility.

Customize the sequencing order form

Use Admin → Form Builder to customize the fields researchers see when creating sequencing orders. You can add, remove, or reorder fields and field groups.

A separate Study Form Builder is available for customizing study metadata forms.

Set up data storage

Storage settings live under Admin → Data Compute (Infrastructure) → Data Storage (/admin/data-storage) — the Data Compute page itself is just a hub that links out to storage and pipeline runtime. There, or via the config file, set:

• Data Base Path — the directory where sequencing files are stored
• File Extensions — which file types to scan for (default: .fastq.gz, .fq.gz, .fastq, .fq)
• Scan Depth — how many directory levels to search (default: 2)

Configure pipelines (optional)

If you plan to run bioinformatics pipelines:

1. Go to Admin → Pipeline Runtime
2. Set the execution mode — local or slurm
3. Configure Conda path and environment if using Conda
4. Configure SLURM queue, cores, memory, and time limit if using SLURM
5. Enable the pipeline features in Admin → Modules

Set up ENA credentials (optional)

If you plan to submit to the European Nucleotide Archive:

1. Go to Admin → ENA Configuration
2. Enter your Webin username and password
3. Set your center name
4. Start with Test Mode enabled to validate submissions against the test server

Review the sequencing order

The sequencing order appears on your Sequencing Orders page (you can see all sequencing orders as admin). Review the sample metadata and sequencing parameters.

Assign sequencing files

After sequencing, go to the Files page to browse the data directory. The system auto-detects FASTQ files and pairs R1/R2 reads. Assign files to the corresponding samples on the sequencing order.

Create a study

Go to Studies and create a new study. Assign the relevant samples from the sequencing order. The study groups samples for pipeline analysis and ENA submission.

Run a pipeline

From the study page, launch a pipeline. SeqDesk generates the samplesheet automatically from the assigned samples and files. Monitor progress in real time through the DAG visualization and weblog events.