diff --git a/db_dockerfiles/vdb/Dockerfile b/db_dockerfiles/vdb/Dockerfile index 3f16ea19..e6129686 100644 --- a/db_dockerfiles/vdb/Dockerfile +++ b/db_dockerfiles/vdb/Dockerfile @@ -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"] diff --git a/db_dockerfiles/vvsr/Dockerfile b/db_dockerfiles/vvsr/Dockerfile index 8d1811ff..1744ff86 100644 --- a/db_dockerfiles/vvsr/Dockerfile +++ b/db_dockerfiles/vvsr/Dockerfile @@ -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 diff --git a/db_dockerfiles/vvta/Dockerfile b/db_dockerfiles/vvta/Dockerfile index 0706e8cb..a9927975 100644 --- a/db_dockerfiles/vvta/Dockerfile +++ b/db_dockerfiles/vvta/Dockerfile @@ -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 diff --git a/docs/INSTALLATION.md b/docs/INSTALLATION.md index 6e015014..8b10f9cc 100644 --- a/docs/INSTALLATION.md +++ b/docs/INSTALLATION.md @@ -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 ``` @@ -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 ``` @@ -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 -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 -v ON_ERROR_STOP=1 -d vvta -Eae ``` diff --git a/docs/INSTALLATION_WINDOWS.md b/docs/INSTALLATION_WINDOWS.md index 735d2f04..ba444feb 100644 --- a/docs/INSTALLATION_WINDOWS.md +++ b/docs/INSTALLATION_WINDOWS.md @@ -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 ``` @@ -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 ``` @@ -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 -v ON_ERROR_STOP=0 -d vvta -Eae ```