diff --git a/{{cookiecutter.project_name}}/justfile b/{{cookiecutter.project_name}}/justfile
new file mode 100644
index 0000000..0ff37bd
--- /dev/null
+++ b/{{cookiecutter.project_name}}/justfile
@@ -0,0 +1,196 @@
+# On Windows the bash shell that comes with Git for Windows should be used.
+# If it is not on path, give the path to the executable in the following line.
+#set windows-shell := ["C:/Program Files/Git/usr/bin/sh", "-cu"]
+
+# Load environment variables from config.public.mk or specified file
+set dotenv-load := true
+# set dotenv-filename := env_var_or_default("LINKML_ENVIRONMENT_FILENAME", "config.public.mk")
+set dotenv-filename := x'${LINKML_ENVIRONMENT_FILENAME:-config.public.mk}'
+
+
+# List all commands as default command. The prefix "_" hides the command.
+_default: _status
+    @just --list
+
+# Set cross-platform Python shebang line (assumes presence of launcher on Windows)
+shebang := if os() == 'windows' {
+  'py'
+} else {
+  '/usr/bin/env python3'
+}
+
+# Environment variables with defaults
+schema_name := env_var_or_default("LINKML_SCHEMA_NAME", "")
+source_schema_path := env_var_or_default("LINKML_SCHEMA_SOURCE_PATH", "")
+
+sheet_module := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_MODULE", "")
+sheet_ID := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_ID", "")
+sheet_tabs := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_TABS", "")
+sheet_module_path := source_schema_path / sheet_module + ".yaml"
+
+config_yaml := if env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "") == "" {
+  "--config-file " + env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "")
+} else {
+  ""
+}
+gen_doc_args := env_var_or_default("LINKML_GENERATORS_DOC_ARGS", "")
+gen_owl_args := env_var_or_default("LINKML_GENERATORS_OWL_ARGS", "")
+gen_java_args := env_var_or_default("LINKML_GENERATORS_JAVA_ARGS", "")
+gen_ts_args := env_var_or_default("LINKML_GENERATORS_TYPESCRIPT_ARGS", "")
+
+# Directory variables
+src := "src"
+dest := "project"
+pymodel := src / schema_name / "datamodel"
+docdir := "docs"
+exampledir := "examples"
+
+# Show current project status
+_status: _check-config
+    @echo "Project: {{schema_name}}"
+    @echo "Source: {{source_schema_path}}"
+
+# Run initial setup (run this first)
+setup: _check-config _git-init install _gen-project _gen-examples _gendoc _git-add _git-commit
+
+# Install project dependencies
+install:
+    poetry install
+
+# Check project configuration
+_check-config:
+    #!{{shebang}}
+    import os
+    schema_name = os.getenv('LINKML_SCHEMA_NAME')
+    if not schema_name:
+        print('**Project not configured**:\n - See \'.env.public\'')
+        exit(1)
+    print('Project-status: Ok')
+
+# Updates project template and LinkML package
+update: _update-template _update-linkml
+
+# Update project template
+_update-template:
+    cruft update
+
+# Update LinkML to latest version
+_update-linkml:
+    poetry add -D linkml@latest
+
+# Create data harmonizer
+_create-data-harmonizer:
+    npm init data-harmonizer {{source_schema_path}}
+
+# Generate all project files
+alias all := site
+
+# Generate site locally
+site: _gen-project _gendoc
+
+# Deploy site
+deploy: site
+  mkd-gh-deploy
+
+_compile_sheets:
+    @if [ ! -z "${{sheet_module}}" ]; then \
+    	poetry run sheets2linkml --gsheet-id {{sheet_ID}} {{sheet_tabs}} > {{sheet_module_path}}.tmp && \
+        mv {{sheet_module_path}}.tmp {{sheet_module_path}}; \
+    fi
+
+# Generate examples
+_gen-examples:
+    mkdir -p {{exampledir}}
+    cp src/data/examples/* {{exampledir}}
+
+# Generate project files
+_gen-project: _ensure_pymodel_dir _compile_sheets
+    poetry run gen-project {{config_yaml}} -d {{dest}} {{source_schema_path}}
+    mv {{dest}}/*.py {{pymodel}}
+    poetry run gen-pydantic {{source_schema_path}} > "{{pymodel}}/{{schema_name}}_pydantic.py"
+    @if [ ! -z "${{gen_owl_args}}" ]; then \
+      poetry run gen-owl {{gen_owl_args}} {{source_schema_path}} > {{dest}}/owl/{{schema_name}}.owl.ttl || true && \
+      poetry run gen-owl {{gen_owl_args}} {{source_schema_path}} > {{dest}}/owl/{{schema_name}}.owl.ttl || true ; \
+    fi
+    @if [ ! ${{gen_java_args}} ]; then \
+      poetry run gen-java {{gen_java_args}} --output-directory {{dest}}/java/ {{source_schema_path}} || true ; \
+    fi
+    @if [ ! ${{gen_ts_args}} ]; then \
+      poetry run gen-typescript {{gen_ts_args}} {{source_schema_path}} > {{dest}}/typescript/{{schema_name}}.ts || true ; \
+    fi
+
+# Run all tests
+test: _test-schema _test-python _test-examples
+
+# Test schema generation
+_test-schema:
+    poetry run gen-project {{config_yaml}} -d tmp {{source_schema_path}}
+
+# Run Python unit tests
+_test-python:
+    poetry run python -m unittest discover
+
+# Run example tests
+_test-examples: _ensure_examples_output
+    poetry run linkml-run-examples \
+        --output-formats json \
+        --output-formats yaml \
+        --counter-example-input-directory src/data/examples/invalid \
+        --input-directory src/data/examples/valid \
+        --output-directory examples/output \
+        --schema src/pid4cat_model/schema/pid4cat_model.yaml > examples/output/README.md
+
+# Run linting
+lint:
+    poetry run linkml-lint {{source_schema_path}}
+
+# Generate documentation
+_gendoc: _ensure_docdir
+    cp -r {{src}}/docs/files/* {{docdir}}
+    poetry run gen-doc {{gen_doc_args}} -d {{docdir}} {{source_schema_path}}
+
+# Build docs and run test server
+testdoc: _gendoc _serve
+
+# Run documentation server
+_serve:
+    poetry run mkdocs serve
+
+# Initialize and add everything to git
+_git-init-add: _git-init _git-add _git-commit _git-status
+
+# Initialize git repository
+_git-init:
+    git init
+
+# Add files to git
+_git-add:
+    touch .cruft.json
+    git add .
+
+# Commit files to git
+_git-commit:
+    git commit -m 'chore: make setup was run' -a
+
+# Show git status
+_git-status:
+    git status
+
+# Clean all generated files
+clean:
+    rm -rf {{dest}}
+    rm -rf tmp
+    rm -rf {{docdir}}/*
+    rm -rf {{pymodel}}
+
+# Private recipes
+_ensure_pymodel_dir:
+    -mkdir -p {{pymodel}}
+
+_ensure_docdir:
+    -mkdir -p {{docdir}}
+
+_ensure_examples_output:
+    -mkdir -p examples/output
+
+import "project.justfile"
diff --git a/{{cookiecutter.project_name}}/project.justfile b/{{cookiecutter.project_name}}/project.justfile
new file mode 100644
index 0000000..bf84fbc
--- /dev/null
+++ b/{{cookiecutter.project_name}}/project.justfile
@@ -0,0 +1 @@
+## Add your own just recipes here. This is imported by the main justfile.