File manipulation/bioinformatics-type scripts that my colleagues 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.
NOTICE: Some files in this repository are encrypted using git-crypt. git-crypt works on a repository-wide basis, meaning that decryption must occur on the entire repository.
sudo apt-get install git-crypt -y
sudo yum install git-crypt -y
Install Homebrew first. Then
brew install git-crypt
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, but you cannot use native git-crypt.
Encryption is GPG-based. If your GPG key has been added to the repository (you know if you have access), then run
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."