https://github.com/millironx/sc2-sequencing
File manipulation/bioinformatics-type scripts that my colleagues have found useful in sequencing SARS-CoV2 (SC2).
https://github.com/millironx/sc2-sequencing
bioinformatics-scripts sars-cov-2 whole-genome-sequencing
Last synced: 5 months ago
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File manipulation/bioinformatics-type scripts that my colleagues have found useful in sequencing SARS-CoV2 (SC2).
- Host: GitHub
- URL: https://github.com/millironx/sc2-sequencing
- Owner: MillironX
- License: unlicense
- Created: 2021-03-18T03:51:44.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2021-04-29T01:30:02.000Z (about 5 years ago)
- Last Synced: 2025-02-03T12:18:29.913Z (over 1 year ago)
- Topics: bioinformatics-scripts, sars-cov-2, whole-genome-sequencing
- Language: Julia
- Homepage:
- Size: 80.1 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# SC2 Sequencing Cheats
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.
## 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
under "Copy Just Your Keys."