crypt4gh 1.8.2

GA4GH cryptographic utilities

Crypt4GH Encryption Utility

crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format.

Installation

Python 3.6+ required to use the crypt4gh encryption utility.

Install it from PyPI:

pip install crypt4gh

or compile and install it from the latest sources

Usage

The usual -h flag shows you the different options that the tool accepts.

$ crypt4gh -h

Utility for the cryptographic GA4GH standard, reading from stdin and outputting to stdout.

Usage:
   {PROG} [-hv] [--log <file>] encrypt [--sk <path>] --recipient_pk <path> [--recipient_pk <path>]... [--range <start-end>]  [--header <path>]
   {PROG} [-hv] [--log <file>] decrypt [--sk <path>] [--sender_pk <path>] [--range <start-end>]
   {PROG} [-hv] [--log <file>] rearrange [--sk <path>] --range <start-end>
   {PROG} [-hv] [--log <file>] reencrypt [--sk <path>] --recipient_pk <path> [--recipient_pk <path>]... [--trim] [--header-only]

Options:
   -h, --help             Prints this help and exit
   -v, --version          Prints the version and exits
   --log <file>           Path to the logger file (in YML format)
   --sk <keyfile>         Curve25519-based Private key.
                          When encrypting, if neither the private key nor C4GH_SECRET_KEY are specified, we generate a new key 
   --recipient_pk <path>  Recipient's Curve25519-based Public key
   --sender_pk <path>     Peer's Curve25519-based Public key to verify provenance (akin to signature)
   --range <start-end>    Byte-range either as  <start-end> or just <start> (Start included, End excluded)
   -t, --trim             Keep only header packets that you can decrypt
   --header <path>        Where to write the header (default: stdout)
   --header-only          Whether the input data consists only of a header (default: false)


Environment variables:
   C4GH_LOG         If defined, it will be used as the default logger
   C4GH_SECRET_KEY  If defined, it will be used as the default secret key (ie --sk ${C4GH_SECRET_KEY})
 

Demonstration

Alice and Bob generate both a pair of public/private keys.

$ crypt4gh-keygen --sk alice.sec --pk alice.pub
$ crypt4gh-keygen --sk bob.sec --pk bob.pub

Bob encrypts a file for Alice:

$ crypt4gh encrypt --sk bob.sec --recipient_pk alice.pub < file > file.c4gh

Alice decrypts the encrypted file:

$ crypt4gh decrypt --sk alice.sec < file.c4gh

File Format

Refer to the specifications or this documentation.

Compilation from sources

Get the source code, and install the python dependencies with:

git clone --recursive https://github.com/EGA-archive/crypt4gh
pip install -r crypt4gh/requirements.txt

The Crypt4GH python package relies on libsodium, a portable C library. A copy is bundled with Crypt4GH as a submodule. You can either use the version of libsodium already installed on your system (eg, provided by your distribution), or use the bundled version.

For the system-wide version, you use the SODIUM_INSTALL=system environment variable. You might also need to adjust the CFLAGS and LDFLAGS environment variables. For example, using pkg-config to find the libsodium headers and library, you can use:

export SODIUM_INSTALL=system
# If not installed in default locations
export CFLAGS="$(pkg-config --cflags libsodium)"
export LDFLAGS="$(pkg-config --libs libsodium)"

If you want to use the bundled version, skip those environment variables.

Finally, run

pip install ./crypt4gh

Bash completions

If you use bash and want auto-completions, you can install the 2 extra scripts, by setting the environment variable CRYPT4GH_BASH_COMPLETIONS to the proper locations for your setup.

For example, if you use the default setup for bash-completion >= 2.x, you can install them with:

export CRYPT4GH_BASH_COMPLETIONS='~/.local/share/bash-completion/completions'
# before you run
pip install ...

If you don't use bash, help me out with a PR and add crypt4gh.zsh, crypt4gh.tcsh, etc... and instructions