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crypt4gh

Build Status CodeFactor

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