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julesjacobsenjulesjacobsen
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Update exomiser install to add a ~/.exomiser and ~/.exomiser/data directories and automatically setup the application.properties to read from this location.
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‎Formula/exomiser.rb‎

Lines changed: 76 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -3,98 +3,114 @@ class Exomiser < Formula
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homepage "https://github.com/exomiser/Exomiser/"
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version "14.1.0"
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# Distribution zip from the Monarch Initiative data repository.
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# Data release version is independent of the application version.
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# Update both constants when releasing a new version.
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DATA_VERSION = "2512"
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#DATA_BASE_URL = "https://data.monarchinitiative.org/exomiser/latest"
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DATA_BASE_URL = "https://g-879a9f.f5dc97.75bc.dn.glob.us/data"
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# Distribution zip from GitHub
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# Update the URL and sha256 checksum when a new version is released.
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url "https://github.com/exomiser/Exomiser/releases/download/#{version}/exomiser-cli-#{version}-distribution.zip"
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sha256 "fb9705017000b448b1331cfd5e1b17c8941713b8c29e4ac30524e96869224db6"
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license "AGPL-3.0"
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# Exomiser requires Java 21 or above.
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depends_on "openjdk@25"
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depends_on "openjdk"
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# No compiled code — Exomiser ships as a pre-built JAR.
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def install
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# Install the JAR and bundled configuration/example files.
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libexec.install Dir["*"]
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# Create a wrapper script using Homebrew's idiomatic method.
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# --sun-misc-unsafe-memory-access=allow suppresses JVM warnings from native libraries that use internal Java APIs.
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bin.write_jar_script libexec/"exomiser-cli-#{version}.jar", "exomiser",
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"-Dspring.config.location=#{libexec}/application.properties"
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end
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libexec.install Dir["*"]
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def caveats
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<<~EOS
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Exomiser has been installed, but it requires large data files to run.
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# Set up ~/.exomiser/data and seed application.properties at install time.
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exomiser_home = Pathname.new(Dir.home)/".exomiser"
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exomiser_data = exomiser_home/"data"
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exomiser_config = exomiser_home/"application.properties"
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─────────────────────────────────────────────────────────────────────
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NEXT STEPS: Download the Exomiser data files
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─────────────────────────────────────────────────────────────────────
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exomiser_data.mkpath unless exomiser_data.exist?
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1. Create a directory to hold the data (80+ GB required):
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unless exomiser_config.exist?
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config = (libexec/"application.properties").read
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config = config.sub(/^exomiser\.data-directory=.*$/, "exomiser.data-directory=#{exomiser_data}")
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config = config.sub(/^#?\s*exomiser\.hg19\.data-version=.*$/, "exomiser.hg19.data-version=#{DATA_VERSION}")
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config = config.sub(/^#?\s*exomiser\.hg38\.data-version=.*$/, "exomiser.hg38.data-version=#{DATA_VERSION}")
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config = config.sub(/^#?\s*exomiser\.phenotype\.data-version=.*$/, "exomiser.phenotype.data-version=#{DATA_VERSION}")
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exomiser_config.write config
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end
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mkdir -p ~/exomiser-data
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bin.write_jar_script libexec/"exomiser-cli-#{version}.jar", "exomiser",
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"--sun-misc-unsafe-memory-access=allow -Dspring.config.location=#{exomiser_home}/application.properties"
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end
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2. Download the data files (this will take a while):
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def caveats
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<<~EOS
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Exomiser has been installed. ~/.exomiser/application.properties and
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~/.exomiser/data have been created and pre-configured for you.
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https://github.com/exomiser/Exomiser/discussions/categories/data-release
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─────────────────────────────────────────────────────────────────────
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NEXT STEPS: Download the Exomiser data files (~80 GB)
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─────────────────────────────────────────────────────────────────────
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cd ~/exomiser-data
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curl -O https://data.monarchinitiative.org/exomiser/latest/2402_phenotype.zip
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Download the phenotype data (required for all analyses):
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# Download one or both genome assemblies depending on your VCF:
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curl -O https://data.monarchinitiative.org/exomiser/latest/2402_hg38.zip
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curl -O https://data.monarchinitiative.org/exomiser/latest/2402_hg19.zip
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wget #{DATA_BASE_URL}/#{DATA_VERSION}_phenotype.zip -P ~/.exomiser/data
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unzip ~/.exomiser/data/#{DATA_VERSION}_phenotype.zip -d ~/.exomiser/data
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3. Unzip the data files:
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Download the genome assembly data for your VCF file.
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If unsure, download both (each ~35 GB):
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unzip '2402_*.zip' -d ~/exomiser-data
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# hg38 (GRCh38)
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wget #{DATA_BASE_URL}/#{DATA_VERSION}_hg38.zip -P ~/.exomiser/data
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unzip ~/.exomiser/data/#{DATA_VERSION}_hg38.zip -d ~/.exomiser/data
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4. Configure Exomiser to find the data. Open:
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# hg19 (GRCh37)
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wget #{DATA_BASE_URL}/#{DATA_VERSION}_hg19.zip -P ~/.exomiser/data
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unzip ~/.exomiser/data/#{DATA_VERSION}_hg19.zip -d ~/.exomiser/data
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#{libexec}/application.properties
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Your data directory should then look like this:
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and set the data directory and version, for example:
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~/.exomiser/data/
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├── #{DATA_VERSION}_phenotype
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├── #{DATA_VERSION}_hg38
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└── #{DATA_VERSION}_hg19
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exomiser.data-directory=#{Dir.home}/exomiser-data
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exomiser.hg38.data-version=2402
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exomiser.phenotype.data-version=2402
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─────────────────────────────────────────────────────────────────────
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CONFIGURATION
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─────────────────────────────────────────────────────────────────────
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5. Run a test analysis to confirm everything is working:
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~/.exomiser/application.properties is pre-configured to point at
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~/.exomiser/data with data version #{DATA_VERSION}. You only need to
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edit it if you store data elsewhere or use a different data release.
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exomiser analyse --analysis #{libexec}/examples/preset-exome-analysis.yml \
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--vcf #{libexec}/examples/Pfeiffer.vcf.gz --assembly hg19 \
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--sample #{libexec}/examples/pfeiffer-phenopacket.yml
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─────────────────────────────────────────────────────────────────────
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TEST YOUR INSTALLATION
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─────────────────────────────────────────────────────────────────────
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─────────────────────────────────────────────────────────────────────
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MEMORY
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─────────────────────────────────────────────────────────────────────
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Once the data is downloaded, confirm everything is working:
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By default the JVM allocates a fraction of available system RAM.
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For genome-scale analyses you may need more. Set JAVA_TOOL_OPTIONS
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before running exomiser to override this, for example:
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exomiser analyse --analysis #{libexec}/examples/test-analysis-exome.yml
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export JAVA_TOOL_OPTIONS="-Xmx12g"
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─────────────────────────────────────────────────────────────────────
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MEMORY
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─────────────────────────────────────────────────────────────────────
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─────────────────────────────────────────────────────────────────────
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FURTHER INFORMATION
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─────────────────────────────────────────────────────────────────────
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For genome-scale analyses you may need to increase JVM memory.
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Set JAVA_TOOL_OPTIONS before running, for example:
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Exomiser Homebrew documentation:
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https://exomiser.readthedocs.io/en/stable/installation.html#linux-macos-installation-via-homebrew
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export JAVA_TOOL_OPTIONS="-Xmx12g"
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Full documentation:
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https://exomiser.readthedocs.io
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─────────────────────────────────────────────────────────────────────
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FURTHER INFORMATION
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─────────────────────────────────────────────────────────────────────
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Data releases and discussions:
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https://github.com/exomiser/Exomiser/discussions/categories/data-release
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EOS
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end
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Full documentation : https://exomiser.readthedocs.io
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Data releases : https://github.com/exomiser/Exomiser/discussions/categories/data-release
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EOS
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end
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test do
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# Verify the wrapper script invokes Java and prints the Exomiser version.
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# This does not require data files to be present.
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output = shell_output("#{bin}/exomiser --version 2>&1", 0)
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assert_match version.to_s, output
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test do
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output = shell_output("#{bin}/exomiser --version 2>&1", 0)
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assert_match version.to_s, output
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end
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end
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end

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