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<ol class="chapter"><li class="chapter-item expanded "><a href="0_intro.html"><strong aria-hidden="true">1.</strong> Introduction</a></li><li class="chapter-item expanded "><a href="1_installation.html"><strong aria-hidden="true">2.</strong> Installation</a></li><li class="chapter-item expanded "><a href="2_encryption.html"><strong aria-hidden="true">3.</strong> Encryption</a></li><li class="chapter-item expanded "><a href="3_key_format.html"><strong aria-hidden="true">4.</strong> Key Format</a></li><li class="chapter-item expanded "><a href="4_usage_and_examples.html" class="active"><strong aria-hidden="true">5.</strong> Usage & Examples</a></li><li class="chapter-item expanded "><a href="5_rust_library.html"><strong aria-hidden="true">6.</strong> Rust Library</a></li></ol> </div>
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<h1 class="menu-title">Crypt4GH Format</h1>
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<h1 id="usage--examples"><a class="header" href="#usage--examples">Usage & Examples</a></h1>
<p>The usual <code>--help</code> flag shows you the different options that the tool accepts.</p>
<pre><code class="language-text">$ crypt4gh --help
Utility for the cryptographic GA4GH standard, reading from stdin and outputting to stdout.
USAGE:
crypt4gh [FLAGS] [SUBCOMMAND]
FLAGS:
-h, --help Prints help information
-v, --verbose Sets the level of verbosity
-V, --version Prints version information
SUBCOMMANDS:
decrypt Decrypts the input using your secret key and the (optional) public key of the sender.
encrypt Encrypts the input using your (optional) secret key and the public key of the recipient.
help Prints this message or the help of the given subcommand(s)
keygen Utility to create Crypt4GH-formatted keys.
rearrange Rearranges the input according to the edit list packet.
reencrypt Decrypts the input using your (optional) secret key and then it reencrypts it using the
public key of the recipient.
</code></pre>
<h2 id="keygen"><a class="header" href="#keygen">Keygen</a></h2>
<pre><code class="language-text">$ crypt4gh keygen --help
crypt4gh-keygen
Utility to create Crypt4GH-formatted keys.
USAGE:
crypt4gh keygen [FLAGS] [OPTIONS]
FLAGS:
-f Overwrite the destination files
-h, --help Prints help information
--nocrypt Do not encrypt the private key. Otherwise it is encrypted in the Crypt4GH key
format (See https://crypt4gh.readthedocs.io/en/latest/keys.html)
-V, --version Prints version information
OPTIONS:
-C, --comment <comment> Key's Comment
--pk <keyfile> Curve25519-based Public key [env: C4GH_PUBLIC_KEY] [default:
~/.c4gh/key.pub]
--sk <keyfile> Curve25519-based Private key [env: C4GH_SECRET_KEY] [default:
~/.c4gh/key]
</code></pre>
<p>Generate a Crypt4GH Key for Alice and Bob.</p>
<pre><code class="language-sh">crypt4gh keygen --sk alice.sec --pk alice.pub
</code></pre>
<pre><code class="language-sh">crypt4gh keygen --sk bob.sec --pk bob.pub
</code></pre>
<h2 id="encrypt"><a class="header" href="#encrypt">Encrypt</a></h2>
<pre><code class="language-text">$ crypt4gh encrypt --help
crypt4gh-encrypt
Encrypts the input using your (optional) secret key and the public key of the recipient.
USAGE:
crypt4gh encrypt [OPTIONS] --recipient_pk <path>...
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
--range <start-end> Byte-range either as <start-end> or just <start> (Start
included, End excluded)
--recipient_pk <path>... Recipient's Curve25519-based Public key
--sk <path> Curve25519-based Private key [env: C4GH_SECRET_KEY]
</code></pre>
<p>Alice encrypts a file <code>file.txt</code> for Bob:</p>
<pre><code class="language-sh">crypt4gh encrypt --sk alice.sec --recipient_pk bob.pub < original_file.txt > encrypted_file.c4gh
</code></pre>
<h2 id="decrypt"><a class="header" href="#decrypt">Decrypt</a></h2>
<pre><code class="language-text">$ crypt4gh decrypt --help
crypt4gh-decrypt
Decrypts the input using your secret key and the (optional) public key of the sender.
USAGE:
crypt4gh decrypt [OPTIONS]
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
--sender_pk <path> Peer's Curve25519-based Public key to verify provenance (akin to
signature)
--sk <path> Curve25519-based Private key. [env: C4GH_SECRET_KEY]
</code></pre>
<p>Bob decrypts an encrypted file:</p>
<pre><code class="language-sh">crypt4gh decrypt --sk bob.sec < encrypted_file.c4gh > decrypted_file.txt
</code></pre>
<p>If Bob wants to, optionally, verify that the message indeed comes from Alice, he needs to fetch Alice's public key via another trusted channel. He can then decrypt and check the provenance of the file with:</p>
<pre><code class="language-sh">crypt4gh decrypt --sk bob.sec --sender_pk alice.pub < encrypted_file.c4gh > decrypted_file.txt
</code></pre>
<h2 id="reencrypt"><a class="header" href="#reencrypt">Reencrypt</a></h2>
<pre><code class="language-text">$ crypt4gh reencrypt --help
crypt4gh-reencrypt
Decrypts the input using your (optional) secret key and then it reencrypts it using the public key
of the recipient.
USAGE:
crypt4gh reencrypt [FLAGS] [OPTIONS] --recipient_pk <path>...
FLAGS:
-h, --help Prints help information
-t, --trim Keep only header packets that you can decrypt
-V, --version Prints version information
OPTIONS:
--recipient_pk <path>... Recipient's Curve25519-based Public key
--sk <path> Curve25519-based Private key [env: C4GH_SECRET_KEY]
</code></pre>
<p>Bob reencrypts a file for alice and for himself:</p>
<pre><code class="language-sh">crypt4gh reencrypt --sk bob.sec --recipient_pk alice.pub bob.pub < encrypted_file.c4gh > reencrypted_file.c4gh
</code></pre>
<h2 id="rearrange"><a class="header" href="#rearrange">Rearrange</a></h2>
<pre><code class="language-text">$ crypt4gh rearrange --help
crypt4gh-rearrange
Rearranges the input according to the edit list packet.
USAGE:
crypt4gh rearrange [OPTIONS] --range <start-end>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
--range <start-end> Byte-range either as <start-end> or just <start> (Start included,
End excluded)
--sk <path> Curve25519-based Private key [env: C4GH_SECRET_KEY]
</code></pre>
<p>Bob rearranges an encrypted file with the bytes from 65535 to 131074:</p>
<pre><code class="language-sh">crypt4gh rearrange --sk bob.sec --range 65535-131074 < encrypted_file.c4gh > rearranged_file.c4gh
</code></pre>
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