Changes for issue #646 - Update docs and application.properties with correct values.

Delete genome_data_version and phenotype_data_version from conf.py as these never worked

Author: julesjacobsen

docs/conf.py

@@ -60,8 +60,6 @@
 
 # The short X.Y version
 version = u'15.1.1'
-genome_data_version = u'2602'
-phenotype_data_version = u'2602'
 # The full version, including alpha/beta/rc tags
 release = version
 

docs/installation.rst

@@ -51,9 +51,9 @@ Before you begin, here are a few terms used throughout this guide:
   Exomiser where your data files are stored and which versions to use.
   You will edit this file as part of setup.
 
-- **Data version (e.g. 2512):** Exomiser data files are released
+- **Data version (e.g. 2602):** Exomiser data files are released
   periodically. The number refers to the year and month of release
-  (e.g. 2512 = February 2024). Your ``application.properties`` must
+  (e.g. 2602 = February 2026). Your ``application.properties`` must
   reference the version you downloaded.
 
 
@@ -82,43 +82,43 @@ and install 7-Zip from http://www.7-zip.org before proceeding.
 **Step 2: Download the files**
 Go to https://github.com/exomiser/Exomiser/releases/latest and download:
 
-- ``exomiser-cli-|version|-distribution.zip`` (the program)
-- ``2512_phenotype.zip`` (required for all analyses)
-- ``2512_hg19.zip`` and/or ``2512_hg38.zip`` (download whichever matches
+- exomiser-cli-\ |version|\-distribution.zip (the program)
+- 2602_phenotype.zip (required for all analyses)
+- 2602_hg19.zip and/or 2602_hg38.zip (download whichever matches
   your VCF file; download both if unsure)
 
 **Step 3: Extract the program**
 
-Right-click ``exomiser-cli-|version|-distribution.zip`` and choose
+Right-click exomiser-cli-\ |version|\-distribution.zip and choose
 **7-Zip > Extract Here**. This will create a folder called
-``exomiser-cli-|version|`` in the same location.
+exomiser-cli-\ |version|\ in the same location.
 
 **Step 4: Extract the data files**
 
-Right-click each data ``.zip`` file (e.g. ``2512_phenotype.zip``,
-``2512_hg19.zip``) and choose **7-Zip > Extract files...**. Extract them
-into the ``data`` subfolder inside your Exomiser folder, e.g.:
+Right-click each data .zip file (e.g. 2602_phenotype.zip,
+2602_hg19.zip) and choose **7-Zip > Extract files...**. Extract them
+into the data/ subfolder inside your Exomiser folder, e.g.:
 
 .. parsed-literal::
 
     exomiser-cli-\ |version|\/data
 
 **Step 5: Configure application.properties**
 
-Open the file ``exomiser-cli-|version|\application.properties`` in a text
+Open the file exomiser-cli-|version|\application.properties in a text
 editor (e.g. Notepad). Find the data version lines and make sure they match
-the version you downloaded (e.g. ``2512``):
+the version you downloaded (e.g. 2602):
 
 .. code-block:: properties
 
-    exomiser.hg19.data-version=2512
-    exomiser.phenotype.data-version=2512
+    exomiser.hg19.data-version=2602
+    exomiser.phenotype.data-version=2602
 
 If you downloaded hg38 instead of (or as well as) hg19, also add or update:
 
 .. code-block:: properties
 
-    exomiser.hg38.data-version=2512
+    exomiser.hg38.data-version=2602
 
 Save the file.
 
@@ -150,15 +150,15 @@ internet speed.
 
     # Download the data files (large — allow several hours)
     # If you only need one genome assembly, download only the relevant file.
-    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_phenotype.zip
-    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_hg38.zip
-    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_hg19.zip
+    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2602_phenotype.zip
+    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2602_hg38.zip
+    wget https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2602_hg19.zip
 
     # Extract the program
     unzip exomiser-cli-\ |version|\-distribution.zip
 
     # Extract the data files into the data subdirectory
-    unzip 2512_*.zip -d exomiser-cli-\ |version|\/data
+    unzip 2602_*.zip -d exomiser-cli-\ |version|\/data
 
     # Navigate into the Exomiser folder
     cd exomiser-cli-\ |version|
@@ -170,14 +170,14 @@ and confirm the data version lines match what you downloaded:
 
 .. code-block:: properties
 
-    exomiser.hg19.data-version=2512
-    exomiser.phenotype.data-version=2512
+    exomiser.hg19.data-version=2602
+    exomiser.phenotype.data-version=2602
 
 Add or update the hg38 line if you downloaded that assembly:
 
 .. code-block:: properties
 
-    exomiser.hg38.data-version=2512
+    exomiser.hg38.data-version=2602
 
 Save and close the file.
 
@@ -246,34 +246,34 @@ Your data directory should look something like this (using ``tree -L 1 /data/exo
 .. code-block:: bash
 
     /data/exomiser-data/
-    ├── 2512_hg19
-    ├── 2512_hg38
-    └── 2512_phenotype
+    ├── 2602_hg19
+    ├── 2602_hg38
+    └── 2602_phenotype
 
 A minimal ``application.properties`` for hg19 exome analysis:
 
 .. code-block:: properties
 
     exomiser.data-directory=/data/exomiser-data
-    exomiser.hg19.data-version=2512
-    exomiser.phenotype.data-version=2512
+    exomiser.hg19.data-version=2602
+    exomiser.phenotype.data-version=2602
 
 For hg38 only:
 
 .. code-block:: properties
 
     exomiser.data-directory=/data/exomiser-data
-    exomiser.hg38.data-version=2512
-    exomiser.phenotype.data-version=2512
+    exomiser.hg38.data-version=2602
+    exomiser.phenotype.data-version=2602
 
 For both assemblies:
 
 .. code-block:: properties
 
     exomiser.data-directory=/data/exomiser-data
-    exomiser.hg19.data-version=2512
-    exomiser.hg38.data-version=2512
-    exomiser.phenotype.data-version=2512
+    exomiser.hg19.data-version=2602
+    exomiser.hg38.data-version=2602
+    exomiser.phenotype.data-version=2602
 
 .. note::
 
@@ -293,8 +293,8 @@ different configurations without editing the file. For example:
 .. parsed-literal::
 
     java -Dexomiser.data-directory=/full/path/to/exomiser-data \
-      -Dexomiser.hg19.data-version=\ |genome_data_version| \
-      -Dexomiser.phenotype.data-version=\ |phenotype_data_version| \
+      -Dexomiser.hg19.data-version=2602 \
+      -Dexomiser.phenotype.data-version=2602 \
       -jar exomiser-cli-\ |version|\.jar analyse --sample examples/pfeiffer-phenopacket.yml
 
 Command-line settings take priority over ``application.properties``.
@@ -304,7 +304,7 @@ with the JAVA_TOOL_OPTIONS environment variable e.g.
 
 .. code-block:: bash
 
-    export JAVA_TOOL_OPTIONS="-Dexomiser.data-directory=/full/path/to/exomiser-data -Dexomiser.hg38.data-version=2512"
+    export JAVA_TOOL_OPTIONS="-Dexomiser.data-directory=/full/path/to/exomiser-data -Dexomiser.hg38.data-version=2602"
 
 Alternatively, Exomiser will recognise exomiser-specific environment variables, as named in the
 ``application.properties`` file e.g.
@@ -484,8 +484,8 @@ allocation by raising the ``-Xmx`` value. For genome analysis, try
 **Exomiser cannot find data files**
 
 Double-check that the version numbers in ``application.properties``
-(e.g. ``exomiser.hg19.data-version=2512``) exactly match the folder names
-in your data directory (e.g. ``2512_hg19``). Even a small mismatch will
+(e.g. ``exomiser.hg19.data-version=2602``) exactly match the folder names
+in your data directory (e.g. ``2602_hg19``). Even a small mismatch will
 cause Exomiser to fail.
 
 **Analysis produces no results**

exomiser-cli/src/main/resources/application.properties

@@ -42,7 +42,7 @@ exomiser.hg19.data-version=${genome.data.version}
 # You will require the tsv.gz and tsv.gz.tbi (tabix) file pairs.
 # Un-comment and add the full path to the relevant tsv.gz files if you want to enable these.
 #exomiser.hg19.cadd-snv-path=${exomiser.data-directory}/cadd/${cadd.version}/hg19/whole_genome_SNVs.tsv.gz
-#exomiser.hg19.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/hg19/InDels.tsv.gz
+#exomiser.hg19.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/hg19/gnomad.genomes-exomes.r4.0.indel.tsv.gz
 #exomiser.hg19.remm-path=${exomiser.data-directory}/remm/ReMM.v${remm.version}.hg19.tsv.gz
 # local frequencies are required to be normalised in the same manner as the input VCF and frequency values must be percentages.
 #exomiser.hg19.local-frequency-path=${exomiser.data-directory}/local/local_frequency_test_hg19.tsv.gz
@@ -54,7 +54,7 @@ exomiser.hg19.data-version=${genome.data.version}
 # To enable analysis of samples called against the hg38 assembly copy the hg19 above and just replace the hg19 with hg38
 #exomiser.hg38.data-version=${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.cadd-in-del-path=${exomiser.data-directory}/cadd/${cadd.version}/gnomad.genomes.r4.0.indel.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