Manual Data Upload to Server

Why

Sometimes you would prefer to use command line tools like scp to 'bulk-copy' your data to the instance, rather than use the Browser Upload UI. You can then use the New > From Server Location... button to load your data into the database. Here are some notes on how to do that.

How

SSH into your server to confirm that your key pair is working properly and that you're comfortable with Millstone's structure (see GitHub's main discussion of how to use ssh keys for a primer if you run into key issues). If you followed the default creation guidelines, you likely have a elastic cloud storage instance created as your main storage. This is already mounted and ready to go.

Place the files that you wish to put on the Millstone server into a single folder for ease of use, and use rsync or scp to transfer over the files using the url and login you found early for SSH logins.

With RSYNC

 ```rsync -rav -e "ssh -i /FULL-PATH-TO-KEY" /PATH-TO-FOLDER-YOUR-COMPUTER [email protected]:/PATH-TO-FOLDER-INSTANCE --progress```

• -r indicates that we want to move over a folder *-i indicates that we want to move over using a key */YOUR-KEY is the location of your .pem key
• /PATH-TO-FOLDER-YOUR-COMPUTER is where you put the files millstone wants to use
• YOUR-NODE is the url that amazon gives you (Public DNS on the instances page)
• PATH-TO-FOLDER-INSTANCE is the location of the folder where we want our sequences to go

With SCP

We recommend you use rsync as it is a bit less dumb than scp. But using the same conventions, the scp command should look like this:

```scp -r -i ~/.ssh/YOUR-KEY /PATH-TO-FOLDER-YOUR-COMPUTER [email protected]:/PATH-TO-FOLDER-INSTANCE```

You're done.

Once this is done your files should be on the cloud! Check using ls to make sure everything is there and move on to accessing them through the UI with New > From Server Location... for Reference Genomes and Samples.