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Peter-J-Freeman merged 2 commits into from
Feb 10, 2026
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Develop #779

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bff1010
update to https://data.variantvalidator.org/
Peter-J-Freeman Feb 10, 2026
efd4eea
Merge pull request #778 from openvar/lovd_updates
Peter-J-Freeman Feb 10, 2026
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2 changes: 1 addition & 1 deletion db_dockerfiles/vdb/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,6 @@ RUN rm -rf /var/lib/apt/lists/*
RUN echo '[mysqld]' >> /etc/mysql/my.cnf && \
echo 'max_connections=250' >> /etc/mysql/my.cnf

RUN wget https://www528.lamp.le.ac.uk/vvdata/validator/validator_2025_03.sql.gz -O /docker-entrypoint-initdb.d/validator_2025_03.sql.gz
RUN wget https://data.variantvalidator.org/vvdata/validator/validator_2025_03.sql.gz -O /docker-entrypoint-initdb.d/validator_2025_03.sql.gz

CMD ["mysqld"]
2 changes: 1 addition & 1 deletion db_dockerfiles/vvsr/Dockerfile
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Expand Up @@ -6,7 +6,7 @@ RUN apt-get install -y wget

RUN mkdir -p /usr/local/share/seqdata

RUN wget --output-document=/usr/local/share/seqdata/VV_SR_2025_02.tar https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_2025_02.tar
RUN wget --output-document=/usr/local/share/seqdata/VV_SR_2025_02.tar https://data.variantvalidator.org/vvdata/vv_seqrepo/VV_SR_2025_02.tar

RUN tar -xvf /usr/local/share/seqdata/VV_SR_2025_02.tar --directory /usr/local/share/seqdata

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2 changes: 1 addition & 1 deletion db_dockerfiles/vvta/Dockerfile
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Expand Up @@ -14,7 +14,7 @@ RUN apt-get update && \
RUN echo "shared_buffers = 2GB" > /docker-entrypoint-initdb.d/postgresql.conf

# Step 1: Download the file
RUN wget https://www528.lamp.le.ac.uk/vvdata/vvta/vvta_2025_02_no_seq.sql.gz -O input_file.sql.gz
RUN wget https://data.variantvalidator.org/vvdata/vvta/vvta_2025_02_no_seq.sql.gz -O input_file.sql.gz

# Step 2: Extract the gzipped file
RUN gzip -dq input_file.sql.gz
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14 changes: 7 additions & 7 deletions docs/INSTALLATION.md
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Expand Up @@ -85,10 +85,10 @@ Where:

Download and our pre-populated database to MySQL as follows.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/validator/) and make sure you download and install the most up-to-date version***
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/validator/) and make sure you download and install the most up-to-date version***

```bash
$ wget https://www528.lamp.le.ac.uk/vvdata/validator/validator_202x-xx-xx.sql.gz
$ wget https://data.variantvalidator.org/vvdata/validator/validator_202x-xx-xx.sql.gz
$ gunzip validator_202x-xx-xx.sql.gz
$ mysql validator < validator_202x-xx-xx.sql -u HOST -p
```
Expand All @@ -101,13 +101,13 @@ If you wish to test your installation using pytest (see below) we recommend that

VariantValidator requires a local SeqRepo database. The seqrepo package has already been installed into the virtual environment, but you'll need to download an actual seqrepo database. This can go anywhere on your system drive.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/) and make sure you download and install the most up-to-date version where the required file is
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/vv_seqrepo/) and make sure you download and install the most up-to-date version where the required file is
e.g. VV_SR_2021_2.tar and the numbers indicate the creation date i.e. 2021_02 = February 2021***

```
$ mkdir /path/to/seqrepo
$ cd /path/to/seqrepo
$ wget https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_20xx_xx.tar
$ wget https://data.variantvalidator.org/vvdata/vv_seqrepo/VV_SR_20xx_xx.tar
$ tar -xvf VV_SR_20xx_xx.tar
$ rm VV_SR_20xx_xx.tar
```
Expand All @@ -133,17 +133,17 @@ Where:

To fill this database, download the gzipped uta genetics database, and upload it into psql.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/vvta/) and make sure you download and install the most up-to-date version***
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/vvta/) and make sure you download and install the most up-to-date version***

*Postgres < version 14.0*
```
$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://data.variantvalidator.org/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ gzip -cdq vvta_202x_xx.noseq.psql.gz | psql -U <USER> -v ON_ERROR_STOP=1 -d vvta -Eae
```

*Postgres >= version 14.0*
```
$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ wget --output-document=VVTA_202x_xx.noseq.psql.gz https://data.variantvalidator.org/vvdata/vvta/VVTA_202x_xx.noseq.psql.gz
$ gzip -cdq -k vvta_202x_xx.noseq.psql.gz | sed 's/anyarray/anycompatiblearray/g' | psql -U <USER> -v ON_ERROR_STOP=1 -d vvta -Eae
```

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12 changes: 6 additions & 6 deletions docs/INSTALLATION_WINDOWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -140,10 +140,10 @@ Where:

Download and our pre-populated database to MySQL as follows.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/validator/) and make sure you download and install the most up-to-date version***
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/validator/) and make sure you download and install the most up-to-date version***

```bash
$ wget https://www528.lamp.le.ac.uk/vvdata/validator/validator_2022_04.sql.gz
$ wget https://data.variantvalidator.org/vvdata/validator/validator_2022_04.sql.gz
$ gunzip validator_2022_04.sql.gz
$ mysql validator < validator_2022_04.sql -u USER -p
```
Expand All @@ -156,13 +156,13 @@ If you wish to test your installation using pytest (see below) we recommend that

VariantValidator requires a local SeqRepo database. The seqrepo package has already been installed into the virtual environment, but you'll need to download an actual seqrepo database. This can go anywhere on your system drive.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/) and make sure you download and install the most up-to-date version where the required file is
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/vv_seqrepo/) and make sure you download and install the most up-to-date version where the required file is
e.g. VV_SR_2021_2.tar and the numbers indicate the creation date i.e. 2021_02 = February 2021***

```
$ mkdir /path/to/seqrepo
$ cd /path/to/seqrepo
$ wget https://www528.lamp.le.ac.uk/vvdata/vv_seqrepo/VV_SR_2022_02.tar
$ wget https://data.variantvalidator.org/vvdata/vv_seqrepo/VV_SR_2022_02.tar
$ tar -xvf VV_SR_2022_02.tar
$ rm VV_SR_2022_02.tar
```
Expand Down Expand Up @@ -197,10 +197,10 @@ Where:

To fill this database, download the gzipped uta genetics database, and upload it into psql.

***Essential Step: check [here](https://www528.lamp.le.ac.uk/vvdata/vvta/) and make sure you download and install the most up-to-date version***
***Essential Step: check [here](https://data.variantvalidator.org/vvdata/vvta/) and make sure you download and install the most up-to-date version***

```
$ wget --output-document=VVTA_2022_02.noseq.sql.gz https://www528.lamp.le.ac.uk/vvdata/vvta/VVTA_2022_02_noseq.sql.gz
$ wget --output-document=VVTA_2022_02.noseq.sql.gz https://data.variantvalidator.org/vvdata/vvta/VVTA_2022_02_noseq.sql.gz
$ gzip -cdq VVTA_2022_02.noseq.psql.gz | psql -U <USER> -v ON_ERROR_STOP=0 -d vvta -Eae
```

Expand Down