First, ensure you have an active AWS account. Install and configure the AWS Command Line Interface (CLI) on your local machine. Use the `aws configure` command to set up your AWS credentials (Access Key ID and Secret Access Key), default region, and output format.

Use Python to download the required package data from PyPI. You can utilize the `requests` library to fetch data from PyPI's JSON API. For example, to get the metadata of a package, use:
```python
import requests

package_name = 'example-package'
response = requests.get(f'https://pypi.org/pypi/{package_name}/json')
package_data = response.json()
# Save this data as a JSON file
with open(f'{package_name}.json', 'w') as f:
json.dump(package_data, f)
```

Once you have the JSON file, ensure it is correctly formatted and contains all necessary information you want to transfer to S3. If needed, clean or transform the data using Python's built-in libraries like `json` or `pandas`.

Log in to your AWS Management Console and create a new S3 bucket where you will store the PyPI data. Ensure the bucket name is unique globally. You can also use the AWS CLI:
```bash
aws s3 mb s3://your-bucket-name
```

Use the AWS CLI to upload your JSON file to the S3 bucket. The command is straightforward:
```bash
aws s3 cp example-package.json s3://your-bucket-name/
```

In AWS Glue, create a new crawler to catalog the data in your S3 bucket. Go to the AWS Glue Console, select "Crawlers," and click "Add crawler." Configure the crawler to point to your S3 bucket and specify the data format. Define an IAM role that grants AWS Glue access to the S3 bucket.

Execute the crawler to create metadata tables in the AWS Glue Data Catalog. Once the crawler completes, use AWS Athena to query your data. In Athena, create a new query using the table created by the Glue crawler:
```sql
SELECT * FROM your_table_name
```
This step allows you to analyze the data directly within AWS using SQL-like queries.

By following these steps, you can efficiently move data from PyPI to Amazon S3 and use AWS Glue to manage and query the data without relying on third-party connectors or integrations.