docs: Update Quickstart guide

docs/calypr/.nav.yml

@@ -2,6 +2,7 @@ title: Calypr
 nav:
   - index.md
   - Quick Start Guide: quick-start.md
+  - Quickstart: quickstart/
   - Data: data/
   - Project Management: project-management/
   - Analysis: analysis/

docs/calypr/project-management/calypr-admin/add-users.md

@@ -23,3 +23,11 @@ data-client collaborator add [project_id] user-read-only@example.com
 
 ## 2.  Approvals
 In order to implement these requests, **an authorized user will need to sign** the request before the user can use the remote repository. See `data-client collaborator approve --help`
+
+## 3. Remove a Collaborator
+
+To remove a user from a project:
+
+```sh
+data-client collaborator remove [project_id] user@example.com
+```

docs/calypr/quickstart/.nav.yml

@@ -0,0 +1,7 @@
+title: Quickstart
+
+nav:
+  - index.md
+  - Create a Project: create-project.md
+  - Upload & Download Files: upload-download.md
+  - Manage Collaborators: collaborators.md

docs/calypr/quickstart/collaborators.md

@@ -0,0 +1,103 @@
+---
+title: Manage Collaborators
+---
+
+# Manage Collaborators
+
+Project access in CALYPR uses a request-and-approve model. A project administrator adds a user, and a steward (someone with the `requestor` role at the institution level) approves the request before access is granted.
+
+All collaborator management is done with the `data-client` tool.
+
+---
+
+## Add a Collaborator
+
+```bash
+./data-client collaborator add [project_id] [email] --profile=<profile-name>
+```
+
+Grant **read** access (default):
+
+```bash
+./data-client collaborator add SEQ-MyProject user@example.com --profile=mycommons
+```
+
+Grant **write** access:
+
+```bash
+./data-client collaborator add SEQ-MyProject user@example.com --profile=mycommons --write
+```
+
+If you have admin permissions, auto-approve the request in one step:
+
+```bash
+./data-client collaborator add SEQ-MyProject user@example.com --profile=mycommons --write --approve
+```
+
+---
+
+## Remove a Collaborator
+
+```bash
+./data-client collaborator rm SEQ-MyProject user@example.com --profile=mycommons
+```
+
+Auto-approve the revocation (requires admin):
+
+```bash
+./data-client collaborator rm SEQ-MyProject user@example.com --profile=mycommons --approve
+```
+
+---
+
+## View Pending Requests
+
+See all requests waiting for approval:
+
+```bash
+./data-client collaborator pending --profile=mycommons
+```
+
+---
+
+## Approve a Request
+
+If you are a project administrator or steward, approve a pending request by its ID:
+
+```bash
+./data-client collaborator approve [request_id] --profile=mycommons
+```
+
+---
+
+## List Active Collaborators
+
+List access requests for your project:
+
+```bash
+# All active requests
+./data-client collaborator ls --profile=mycommons --active
+
+# Your own requests
+./data-client collaborator ls --profile=mycommons --mine
+
+# Requests for a specific user (admin only)
+./data-client collaborator ls --profile=mycommons --username=user@example.com
+```
+
+---
+
+## Roles Summary
+
+| Role | Can add collaborators | Can approve requests |
+|---|---|---|
+| Project member | No | No |
+| Project administrator | Yes | Yes (own project) |
+| Institution steward | No | Yes (own institution) |
+
+---
+
+## Next Steps
+
+- [Upload & Download Files](upload-download.md) — share data with your new collaborators
+- [data-client Access & Collaboration](../../tools/data-client/access_requests.md) — full command reference

docs/calypr/quickstart/create-project.md

@@ -0,0 +1,97 @@
+---
+title: Create a Project
+---
+
+# Create a Project
+
+!!! info "Admin-assisted setup"
+    Project creation is currently handled by the CALYPR team. Submit a request and they will provision your project and send you the details you need to get started.
+
+## Step 1 — Request a Project
+
+Email `support@calypr.org` with:
+
+- Your CALYPR account email
+- A short project name and description
+- The institution or program it belongs to
+
+The team will respond with:
+
+| Detail | Example |
+|---|---|
+| GitHub repository URL | `https://github.com/calypr/my-project` |
+| Project ID | `SEQ-MyProject` |
+| DRS server URL | `https://calypr-public.ohsu.edu` |
+| S3 bucket name | `calypr-my-project` |
+
+---
+
+## Step 2 — Install Git DRS
+
+If you haven't already, install Git LFS and Git DRS.
+
+**Initialize Git LFS** (once per machine):
+
+```bash
+git lfs install --skip-smudge
+```
+
+**Install Git DRS:**
+
+```bash
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/calypr/git-drs/refs/heads/main/install.sh)"
+```
+
+Add Git DRS to your PATH:
+
+```bash
+echo 'export PATH="$PATH:$HOME/.local/bin"' >> ~/.bash_profile
+source ~/.bash_profile
+```
+
+---
+
+## Step 3 — Clone and Initialize
+
+Clone the repository provided by the CALYPR team:
+
+```bash
+git clone https://github.com/calypr/my-project.git
+cd my-project
+git drs init
+```
+
+`git drs init` configures the Git hooks needed for DRS-backed file uploads.
+
+---
+
+## Step 4 — Configure the DRS Remote
+
+Use the project details from Step 1:
+
+```bash
+git drs remote add gen3 production \
+    --cred ~/.gen3/credentials.json \
+    --url https://calypr-public.ohsu.edu \
+    --project SEQ-MyProject \
+    --bucket calypr-my-project
+```
+
+Verify the remote was added:
+
+```bash
+git drs remote list
+```
+
+```
+* production  gen3    https://calypr-public.ohsu.edu
+```
+
+The `*` marks your default remote.
+
+---
+
+## Next Steps
+
+- [Upload & Download Files](upload-download.md) — add your first data files
+- [Manage Collaborators](collaborators.md) — invite team members

docs/calypr/quickstart/index.md

@@ -0,0 +1,39 @@
+---
+title: Quickstart
+---
+
+# Quickstart
+
+Get up and running with CALYPR in three steps.
+
+## Prerequisites
+
+Before you begin, make sure you have:
+
+- **Git** installed ([download](https://git-scm.com))
+- **Git LFS** installed — [macOS](https://formulae.brew.sh/formula/git-lfs): `brew install git-lfs` / [Linux/Windows](https://git-lfs.com)
+- **A CALYPR account** — contact your project administrator or email `support@calypr.org`
+- **Gen3 API credentials** downloaded from your [Profile page](https://calypr-public.ohsu.edu/Profile)
+
+!!! tip "API credentials expire every 30 days"
+    Download fresh credentials from your Profile page when they expire and re-run `git drs remote add` to update your configuration.
+
+---
+
+## Steps
+
+<div class="grid cards" markdown>
+
+- :octicons-repo-16: **[1. Create a Project](create-project.md)**
+
+    Request a new project and configure your local repository.
+
+- :octicons-upload-16: **[2. Upload & Download Files](upload-download.md)**
+
+    Add data files using Git-DRS (version-controlled) or the data-client (direct transfer).
+
+- :octicons-people-16: **[3. Manage Collaborators](collaborators.md)**
+
+    Add or remove users from your project and manage access requests.
+
+</div>

docs/calypr/quickstart/upload-download.md

@@ -0,0 +1,116 @@
+---
+title: Upload & Download Files
+---
+
+# Upload & Download Files
+
+CALYPR supports two tools for transferring data files:
+
+| | **Git DRS** | **data-client** |
+|---|---|---|
+| Best for | Version-controlled datasets, collaboration, reproducibility | Direct uploads without Git, scripted pipelines |
+| Requires | Git repository initialized with `git drs init` | A configured `data-client` profile |
+| Output | Files tracked in Git with DRS-backed pointer files | Files indexed in Gen3 (Indexd) with a GUID |
+
+---
+
+## Git DRS (recommended)
+
+Git DRS integrates with your Git repository to track large files. Files are stored in S3 and registered with Gen3's DRS service — only lightweight pointer files live in Git.
+
+### Upload
+
+**1. Track the file type with Git LFS:**
+
+```bash
+git lfs track "*.bam"
+git add .gitattributes
+git commit -m "Track BAM files with Git LFS"
+```
+
+**2. Add, commit, and push:**
+
+```bash
+git add data/sample.bam
+git commit -m "Add sample BAM file"
+git push
+```
+
+On `git push`, Git DRS automatically:
+
+1. Registers a DRS record in Gen3 (indexd)
+2. Uploads the file to S3
+3. Stores the pointer in the Git repository
+
+You can verify tracked files at any time:
+
+```bash
+git lfs ls-files
+```
+
+A `*` next to a file means the content is present locally; `-` means only the pointer is checked out.
+
+### Download
+
+```bash
+# Download all tracked files
+git lfs pull
+
+# Download by pattern
+git lfs pull -I "*.bam"
+
+# Download a specific directory
+git lfs pull -I "data/**"
+```
+
+---
+
+## data-client (direct transfer)
+
+Use the `data-client` when you need to upload or download files outside of a Git workflow, or in batch/scripted scenarios.
+
+### Configure a profile
+
+If you haven't set up a profile yet:
+
+```bash
+./data-client configure --profile=mycommons
+```
+
+You'll be prompted for your Gen3 API endpoint and credentials path.
+
+### Upload
+
+Upload a single file:
+
+```bash
+./data-client upload --profile=mycommons --upload-path=data/sample.bam
+```
+
+Upload a directory in parallel:
+
+```bash
+./data-client upload --profile=mycommons --upload-path=data/ --batch --numparallel=5
+```
+
+Each uploaded file receives a **GUID** (Globally Unique Identifier) from Gen3. Save these GUIDs — they are required to download the files later.
+
+### Download
+
+```bash
+./data-client download --profile=mycommons --guid=dg.1234/5678-abcd
+```
+
+To download to a specific directory:
+
+```bash
+./data-client download --profile=mycommons --guid=dg.1234/5678-abcd --dir=./downloads
+```
+
+---
+
+## Next Steps
+
+- [Manage Collaborators](collaborators.md) — share your project with team members
+- [Git DRS Complete Guide](../../tools/git-drs/quickstart.md) — advanced workflows, multiple remotes, cross-remote promotion
+- [data-client Authentication](../../tools/data-client/authentication.md) — profile setup and access verification