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File preparation

Due to the processes used at the EGA for file archival the use of non-alphanumeric characters in a filename will cause issues in archival. By convention whitespaces in filenames are to be avoided and should be replaced with the underscore character (_). Before encrypting your files please make sure that any files that will be uploaded to EGA do not use special characters such as # ? ( ) [ ] / \ = + < > : ; " ' , * ^ | & 

Files encrypted with EGACryptor must be uploaded via FTP


The EGACryptor v.2.0.0 is a JAVA-based application which enables submitters to produce EGA compliant encrypted files along with files for the encrypted and unencrypted md5sum for each file to be submitted. The application will generate an output folder that will by default mirror the directory structure containing the original files. This output folder can subsequently be uploaded to the EGA FTP staging area via an FTP or Aspera client.

Download EgaCryptor

Download EgaCryptor

Using the EgaCryptor

Using the EgaCryptor

Encrypting single file

Encrypting multiple files

Encrypting all files in folder

Points to note



Download EGACryptor

The required jar files can be obtained by downloading EgaCrytptor jar file

After the file has been downloaded, extraction of the zipped archive is required. The EGACryptor has been built to work with Java Runtime Environments from version 6 and above and with the OpenJDK Environment. Please refer to the relevant resources for installation guidance. Installing the latest version of the OpenJDK will include the JCE files. If your installation of Java JRE is less than 1.8.0_151 will require the manual installation of the JCE Policy Files. You can verify the version of the Java SE Runtime Environment (JRE) installed by using the command:

$ java -version

If you need to install the JCE please follow the instructions below:

Installing the JCE policy files (due to licensing terms and conditions the required policy files must be downloaded direct from the ORACLE website) :

  1. Download the unlimited strength JCE policy files (JRE 6 / JRE 7/ JRE 8)
  2. Uncompress and extract the downloaded file.
  3. This will create a subdirectory called JCE. This directory contains the following files: README.txt, COPYRIGHT.html, local_policy.jar and US_export_policy.jar
  4. Install the two policy JAR files by replacing the existing ones in your java home directory.
  5. Install the two policy JAR files by replacing the existing ones in your directory.
  6. The standard place for JCE jurisdiction policy JAR files is: /lib/security [Unix] or \lib\security [Win32]

Notes: refers to the directory where the Java SE Runtime Environment (JRE) was installed.

Additional performance enhancements that have been included in the EGACryptor V2.0.0:

The tool can only be used via the command line. The EGACryptor is designed to perform a single task, encrypting your data, for upload of these files please refer to our uploading guide

Using the EgaCryptor

Below are the three ways on how the EGACryptor tool can be used:

Encrypting a single file :

java -jar ../EGA-Cryptor_2_0_0.jar -i example1.bam

Encrypting multiple files :

java -jar ../EGA-Cryptor_2_0_0.jar -i "example1.bam,example2.bam"

Encrypting all the files within a folder

java -jar ../EGA-Cryptor_2_0_0.jar -i path/to/target/directory

By default the EGACryptor v2 will create a new output directory containing all encrypted files and the relevant checksums within the target directory. If a specific directory is desired this can be specified by using the -o flag. This can be achieved in a similar manner to the following example:

java -jar ../EGA-Cryptor_2_0_0.jar -i /path/to/target/directory -o /path/to/output/directory

The tool will output three files per input file:

All output files must then be uploaded to your submission account using Aspera or FTP. Further documentation on how to upload files: FTP and Aspera.

Points to note


If in doubt about the function of the EGACryptor it is recommended to first consult the built-in documentation. This can be accessessed by using the -h flag as stated in the following table.

Built-in Commands
Table: list of the command line options built into EGA-Cryptor v2.0.0.
Command line Option    Action
---------------------  -----------
-f                     Set this option to allow application to create maximum
                         threads to utilise full capacity of cores/processors
                         available on machine
-h                     Use this option to view the bult-in help menu
* -i                   File(s) to encrypt. Provide file/folder path or comma
                         separated file path if multiple files in double quotes
-l                     Set this option to allow application to create maximum
                         threads equals to 50% capacity of cores/processors
                         available on machine
-m                     Set this option to allow application to create maximum
                         threads equals to 75% capacity of cores/processors
                         available on machine
-o                     Path of the output file. This is optional. If not
                         provided then output files will be generated in the
                         same path as that of source file (default: output-
-t                     Set this option if user wants to control application to
                         create maximum threads as specified. Application will
                         calculate no. of cores/processors available on machine
                         & will create threads accordingly
Encryption Errors UnixFileSystem.createFileExclusively (Native Method)

The error is thrown by UNIX ("UnixFileSystem.createFileExclusively(Native Method)"). It appears that the user does not have write-access to the file system where the file to be uploaded is located. EGACryptor always writes MD5 checksums into files before uploading them to the server, and these files are created in the same location where the uploaded file itself resides.Solution: address your directory permission issue and re-run the command.

Install JCE Unlimited Strength Jurisdiction Policy files

The JCE policy unlimited strength jurisdiction files should be installed according to your current java version

If you are still facing difficulty with the EGACryptor v.2 after having consulted the documentation please contact the EGA Helpdesk.