Update pom.xml genome.data.version and phenotype.data.version propert…

…ies to 2410 Update cli, prioritiser and web application.properties to use project data.version properties Update exomiser-cli README.md Java version.
exomiser · Nov 13, 2024 · 1dca4e9 · 1dca4e9
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diff --git a/exomiser-cli/README.md b/exomiser-cli/README.md
@@ -13,7 +13,8 @@
 
 # <a id="the-exomiser"></a>The Exomiser - A Tool to Annotate and Prioritize Disease Variants: Command Line Executable
 
-The Exomiser is a tool to perform genome-wide prioritisation of genomic variants including non-coding and regulatory variants using patient phenotypes as a means of differentiating candidate genes.
+The Exomiser is a tool to perform genome-wide prioritisation of genomic variants including non-coding and regulatory
+variants using patient phenotypes as a means of differentiating candidate genes.
 
 To perform an analysis, Exomiser requires the patient's genome/exome in VCF format and their phenotype encoded in HPO
 terms. The exomiser is also capable of analysing trios/small family genomes, so long as a pedigree in PED format is also
@@ -25,7 +26,7 @@ Further information can be found in the [online documentation](https://exomiser.
  - 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 11 or above
+ - Java 17 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).
@@ -121,7 +122,7 @@ See the test-analysis-exome.yml and test-analysis-genome.yml files located in th
 
     java -Xmx4g -jar exomiser-cli-${project.version}.jar --analysis examples/test-analysis-exome.yml
 
-These files an also be used to run full-genomes, however they will require substantially more RAM to do so. For example
+These files can also be used to run full-genomes, however they will require substantially more RAM to do so. For example
 a 4.4 million variant analysis requires approximately 12GB RAM. However, RAM requirements can be greatly reduced by 
 setting the analysisMode option to PASS_ONLY. This will also aid your ability to evaluate the results.
 
@@ -147,7 +148,7 @@ If you get the following error message:
     Exception in thread "main" java.lang.UnsupportedClassVersionError:
     org/monarchinitiative/exomiser/cli/Main : Unsupported major.minor version
 
-You are running an older unsupported version of Java. Exomiser requires java version 11 or higher. This can be checked
+You are running an older unsupported version of Java. Exomiser requires Java version 17 or higher. This can be checked
 by running:
 
     java -version
@@ -158,8 +159,8 @@ You should see something like this in response:
     OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
     OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)
 
-versions lower than 11 (e.g. 1.5, 1.6, 1.7, 1.8, 9, 10) will not run exomiser, so you will need to install the latest
-java version.
+versions lower than 17 (e.g. 1.5, 1.6, 1.7, 1.8, 9, 10, 11...) will not run exomiser, so you will need to install the latest
+LTS Java version. We recommend using the Eclipse Temurin Java releases which you can find here: https://adoptium.net/
 
 ### Zip file reported as too big or corrupted
 

diff --git a/exomiser-cli/src/main/resources/application.properties b/exomiser-cli/src/main/resources/application.properties
@@ -35,7 +35,7 @@ remm.version=0.3.1.post1
 cadd.version=1.4
 
 ### hg19 assembly ###
-exomiser.hg19.data-version=2402
+exomiser.hg19.data-version=${genome.data.version}
 # transcript source will default to ensembl. Can define as ucsc/ensembl/refseq
 #exomiser.hg19.transcript-source=ensembl
 # location of CADD/REMM Tabix files - you will need these for analysis of non-coding variants.
@@ -47,22 +47,22 @@ exomiser.hg19.data-version=2402
 # local frequencies are required to be normalised in the same manner as the input VCF and frequency values must be percentages.
 #exomiser.hg19.local-frequency-path=${exomiser.data-directory}/local/local_frequency_test_hg19.tsv.gz
 #exomiser.hg19.variant-white-list-path=${exomiser.hg19.data-version}_hg19_clinvar_whitelist.tsv.gz
-#exomiser.hg19.clin-var-data-version=2402
+#exomiser.hg19.clin-var-data-version=${genome.data.version}
 #exomiser.hg19.use-clinvar-white-list=true
 
 ### hg38 assembly ###
 # To enable analysis of samples called against the hg38 assembly copy the hg19 above and just replace the hg19 with hg38
-#exomiser.hg38.data-version=2402
+#exomiser.hg38.data-version=${genome.data.version}
 #exomiser.hg38.cadd-snv-path=${exomiser.data-directory}/cadd/${cadd.version}/whole_genome_SNVs.tsv.gz
 #exomiser.hg38.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/InDels.tsv.gz
 #exomiser.hg38.remm-path=${exomiser.data-directory}/remm/ReMM.v${remm.version}.hg38.tsv.gz
 #exomiser.hg38.local-frequency-path=${exomiser.data-directory}/local/local_frequency_test_hg38.tsv.gz
 #exomiser.hg38.variant-white-list-path=${exomiser.hg38.data-version}_hg38_clinvar_whitelist.tsv.gz
-#exomiser.hg38.clin-var-data-version=2402
+#exomiser.hg38.clin-var-data-version=${genome.data.version}
 #exomiser.hg38.use-clinvar-white-list=true
 
 ### phenotypes ###
-exomiser.phenotype.data-version=2402
+exomiser.phenotype.data-version=${phenotype.data.version}
 #exomiser.phenotype.data-directory=${exomiser.data-directory}/${exomiser.phenotype.data-version}_phenotype
 # String random walk data file
 #exomiser.phenotype.random-walk-file-name=rw_string_10.mv
@@ -81,4 +81,4 @@ exomiser.phenotype.data-version=2402
 ### logging ###
 # Logging is highly configurable - see https://docs.spring.io/spring-boot/docs/current/reference/html/features.html#features.logging.file-output
 #logging.file.name=logs/exomiser.log
-logging.level.com.zaxxer.hikari=ERROR
+logging.level.com.zaxxer.hikari=ERROR ${java.version}
diff --git a/exomiser-rest-prioritiser/src/main/resources/application.properties b/exomiser-rest-prioritiser/src/main/resources/application.properties
@@ -25,7 +25,7 @@ server.servlet.application-display-name=Exomiser Prioritiser Server
 
 #Absolute system path where the exomiser data is installed
 exomiser.data-directory=${project.build.testOutputDirectory}
-exomiser.phenotype.data-version=1707
+exomiser.phenotype.data-version=${phenotype.data.version}
 exomiser.phenotype.random-walk-preload=true
 
 #Actuator configuration

diff --git a/exomiser-web/src/main/resources/application.properties b/exomiser-web/src/main/resources/application.properties
@@ -44,7 +44,7 @@ exomiser.web.max-genes=30
 exomiser.web.clinical-instance=false
 # Configure the Exomiser properties - use the exomiser-cli application.properties as a template
 exomiser.data-directory=${data.dir}
-#exomiser.hg19.data-version=2109
+#exomiser.hg19.data-version=${genome.data.version}
 #exomiser.hg19.variant-white-list-path=${exomiser.hg19.data-version}_hg19_clinvar_whitelist.tsv.gz
-#exomiser.phenotype.data-version=2109
+#exomiser.phenotype.data-version=${phenotype.data.version}
 exomiser.phenotype.random-walk-preload=true
diff --git a/pom.xml b/pom.xml
@@ -109,9 +109,9 @@
         </docker.base.image>
         <docker.registry>docker.io</docker.registry>
         <docker.repository>exomiser</docker.repository>
-        <!--    These properties are use for the README.md  -->
-        <genome.data.version>2402</genome.data.version>
-        <phenotype.data.version>2402</phenotype.data.version>
+        <!--    These properties are used for the README.md and updating the application.properties -->
+        <genome.data.version>2410</genome.data.version>
+        <phenotype.data.version>2410</phenotype.data.version>
     </properties>
 
     <dependencyManagement>