sc2-sequencing/README.md

# SC2 Sequencing Cheats

File manipulation/bioinformatics-type scripts that my colleuges have found
useful in sequencing SARS-CoV2 (SC2).

These scripts have various purposes, uses, and instructions. The only unifying
thing about them is that they were all written for SC2 and related sequencing.
Please check the `README` file in each directory for more detailed instructions.

## Encryption

**NOTICE:** Some files in this repository are encrypted using
[git-crypt](https://github.com/AGWA/git-crypt). git-crypt works on a
repository-wide basis, meaning that decryption must occur on the entire
repository.

### Installing git-crypt

#### Ubuntu, Debian, etc.

```bash
sudo apt-get install git-crypt -y
```

#### Fedora, CentOS, RHEL, etc.

```bash
sudo yum install git-crypt -y
```

#### MacOS

Install [Homebrew](https://brew.sh/) first. Then

```bash
brew install git-crypt
```

#### Windows

There are no official git-crypt builds for Windows. I repeat, **git-crypt does
not exist for Windows** regardless of what others may tell you. If possible, you
may use the [Windows Subsystem for
Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10), but you
cannot use native git-crypt.

### Decrypting the repository

Encryption is GPG-based. If your GPG key has been added to the repository (you
know if you have access), then run

```bash
git clone https://github.com/MillironX/sc2-sequencing.git && cd sc2-sequencing
git-crypt unlock
```

The files will now be decrypted and can be usable.

If you need to copy your GPG keys to a new machine to be able to decrypt the
files, follow the instructions at
<https://www.phildev.net/pgp/gpg_moving_keys.html> under "Copy Just Your Keys."