Install from database dump

VG GRCh37/GRCh38 VEP version 112 (RefSeq) on 2024-08-06

Download dump

Data has been installed, migrations run and annotation performed (on ClinVar variants), which reduces the amount of work needed to install

Annotation version warning: this dump was annotated with VEP 112 / columns_version 3, while the current packaged default is VEP 116 / columns_version 5 (see Annotation Column Versions). If you restore it and run with the default settings, every variant needs re-annotating — which is the work the dump was meant to save you.

Two options:

• Install the VEP version matching the dump and pin your settings back with pin_annotation_to_columns_version_3(ANNOTATION), or
• accept the re-annotation (fine for a small test database).

Setting up database

You need to have created a database - see Install step "Create DB" ie:

sudo su postgres -c "psql < variantgrid/scripts/dbscripts/pgsql_database_create.sql"

Restoring dump

The dump's objects are owned by the snpdb user, so restore as that user (this needs the password login set up in Install — -W prompts for the password from /etc/variantgrid/settings_config.json):

wget https://variantgrid.com/download/vg_test_dump-2024-08-06.sql.gz
zcat vg_test_dump-2024-08-06.sql.gz | psql --user snpdb -d snpdb -W

Restore into a freshly created, empty database — before running python3 manage.py migrate, as the dump brings its own schema and migration history with it. Once it's loaded, run migrate to bring the schema up to the version of the code you have checked out.

Annotation Versions

Annotations used correspond to:

https://ftp.ensembl.org/pub/release-112/variation/indexed_vep_cache/homo_sapiens_refseq_vep_112_GRCh37.tar.gz https://ftp.ensembl.org/pub/release-112/variation/indexed_vep_cache/homo_sapiens_refseq_vep_112_GRCh38.tar.gz