Software and Hardware requirements

  • For exome analysis of a 30,000 variant sample 4GB RAM should suffice.
  • For genome analysis of a 4,400,000 variant sample 12GB RAM should suffice.
  • Any 64-bit operating system
  • Java 8 or above
  • At least 50GB free disk space (SSD preferred for best performance)
  • An internet connection is not required to run the Exomiser, although network access will be required if accessing a networked database (optional).
  • By default the Exomiser is completely self-contained and is able to run on standard consumer laptops.

Installation

Windows

  1. Install 7-Zip for unzipping the archive files. The built-in archiving software has issues extracting the zip files.
  2. Download the data and distribution files from the FTP site.
  3. Extract the distribution files by right-clicking exomiser-cli-7.2.3-distribution.zip and selecting 7-Zip > Extract Here
  4. Extract the data files by right-clicking exomiser-cli-7.2.3-data.zip and selecting 7-Zip > Extract Here
    1. Allow 7-Zip to overwite any empty data files with the full versions if prompted (remmData for example)
  5. Use your cmd to test your installation:

     cd exomiser-cli-7.2.3
     java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --analysis NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml
    

Linux

Use the following commands:

  1. Download the distribution (won’t take long)

     wget ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.3-distribution.zip
    
  2. Download the data (this is ~20GB and will take a while)

     wget ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.3-data.zip
    
  3. Download the checksums and verify the files (optional)

     wget ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.3.sha256
     sha256sum -c exomiser-cli-7.2.3.sha256
    
  4. Unzip the distribution and data files - this will create a directory called ‘exomiser-cli-7.2.3’ in the current working directory

     unzip exomiser-cli-7.2.3-distribution.zip
     unzip exomiser-cli-7.2.3-data.zip
    
  5. Run a test genomiser analysis

    cd exomiser-cli-7.2.3
    java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --analysis NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml
    

These commands will download, verify and extract the exomiser files and then run the analysis contained in the file NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml. This file is an analysis for an autosomal recessive 5’UTR variant located in POMP gene on chromosome 13. The phenotype HPO terms are taken from the clinical synopsis of OMIM #601952

Mac

  1. Install http://p7zip.sourceforge.net/

     brew install p7zip
    
  2. Unzip the data:

     7z l exomiser-cli-7.2.1-data.zip
    

Alternative set-up

If you want to run Exomiser using an H2 database from a location of your choosing edit the line in application.properties:

h2Path=

with

h2Path=/full/path/to/alternative/h2/database/exomiser.h2.db