ega-cryptor

Enables submitters to produce EGA compliant files. Multiple files will be processed in parallel. Application will generate 3 files .md5, .gpg and gpg.md5 for each source file respectively.

E.g. After encryption of source_file.bam these files will be generated source_file.bam.md5, source_file.bam.gpg, source_file.bam.gpg.md5

How to run

Make sure Java 1.8 or above version is installed on your system. type java -version and press enter to check what java version is installed. Download the ega-cryptor-2.0.0.jar and navigate to folder in which jar has been downloaded.

• Get help options

  It displays all available options.

  java -jar ega-cryptor-2.0.0.jar --h
  

• Single File To Encrypt

  It will generate output files at same location as that of source file.

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file.bam"
  

  It will generate output files in the target directory specified in outputFolderPath.

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file.bam" --o="/path/to/output/folder"
  

• Multiple Files or/and Folders To Encrypt

  Specify multiple files comma separated. It will generate output files at same location as that of source files.

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/file/tobe/encrypted/file2.bam, /path/to/folder/tobe/encrypted/test1, /path/to/folder/tobe/encrypted/test2"
  

  It will generate output files in the target directory specified in outputFolderPath.

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/folder/tobe/encrypted/test1" --o="/path/to/output/folder"
  

• Process multiple files in parallel - You can specify one of the the 3 options to allow application to determine suitable no. of threads to be created.

  Allow application to use full resource capacity

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/folder/tobe/encrypted/test1" --o="/path/to/output/folder" -f
  

  Allow application to use moderate (75%) resource capacity

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/folder/tobe/encrypted/test1" --o="/path/to/output/folder" -m
  

  Allow application to use low/half (50%) resource capacity

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/folder/tobe/encrypted/test1" --o="/path/to/output/folder" -l
  

  Allow application to use user specified resources/threads

  java -jar ega-cryptor-2.0.0.jar --i="/path/to/file/tobe/encrypted/file1.bam, /path/to/folder/tobe/encrypted/test1" --o="/path/to/output/folder" -t=3
  

  *Note if no option will be provided, application will process files sequenctially using single thread.