crypt4gh

Overview

File structure

Specification

Current version of specs can be found here.

Maven Installation

To include this library to your Maven project add following to the pom.xml:

...

    <dependencies>
        <dependency>
            <groupId>no.uio.ifi</groupId>
            <artifactId>crypt4gh</artifactId>
            <version>VERSION</version>
        </dependency>
    </dependencies>

...

    <repositories>
        <repository>
            <id>github</id>
            <name>uio-bmi-Crypt4GH</name>
            <url>https://maven.pkg.github.com/uio-bmi/crypt4gh</url>
        </repository>
    </repositories>

...

In addition ensure that your settings.xml includes the required github credentials following the github docs. Here's an example:

<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
                      http://maven.apache.org/xsd/settings-1.0.0.xsd">

  <activeProfiles>
    <activeProfile>github</activeProfile>
  </activeProfiles>
  <servers>
    <server>
      <id>github</id>
      <username>my_username</username>
      <password>A_read_token_created_according_to_github_doc</password>
    </server>
  </servers>
  <profiles>
    <profile>
      <id>github</id>
      <repositories>
        <repository>
          <id>central</id>
          <url>https://repo1.maven.org/maven2</url>
        </repository>

        <repository>
          <id>github</id>
          <name>uio-bmi-crypt4gh</name>
          <url>https://maven.pkg.github.com/uio-bmi/crypt4gh/</url>
          <snapshots>
            <enabled>true</enabled>
          </snapshots>
        </repository>

      </repositories>
    </profile>
  </profiles>


</settings>

Console Installation

To install console app you can use the following script (assuming you are using bash):

PREFIX=/usr/local/bin && \
sudo curl -L "https://github.com/uio-bmi/crypt4gh/releases/download/v2.4.8/crypt4gh.jar" -o "$PREFIX/crypt4gh.jar" && \
echo -e '#!/usr/bin/env bash\njava -jar' "$PREFIX/crypt4gh.jar" '$@' | sudo tee "$PREFIX/crypt4gh" > /dev/null && \
sudo chmod +x "$PREFIX/crypt4gh"

Usage

$ crypt4gh 
usage: crypt4gh [-d <arg> | -e <arg> | -g <arg> | -h | -v]    [-kf <arg>]
       [-kp <arg>] [-pk <arg>] [-sk <arg>]

Crypt4GH encryption/decryption tool

 -d,--decrypt <arg>    decrypt the file (specify file to decrypt)
 -e,--encrypt <arg>    encrypt the file (specify file to encrypt)
 -g,--generate <arg>   generate key pair (specify desired key name)
 -h,--help             print this message
 -kf,--keyform <arg>   key format to use for generated keys (OpenSSL or
                       Crypt4GH)
 -kp,--keypass <arg>   password for Crypt4GH private key (will be prompted
                       afterwords if skipped)
 -pk,--pubkey <arg>    public key to use (specify key file)
 -sk,--seckey <arg>    secret key to use (specify key file)
 -v,--version          print application's version

Read more about the format at
http://samtools.github.io/hts-specs/crypt4gh.pdf