The purpose of this project is to collect various annotation database files required by VarFish Web UI and convert them into the format that is required for the import into VarFish Web UI.
git clone [email protected]:CUBI_Engineering/VarFish/varfish-db-downloader
cd varfish-db-downloader
conda env create -f environment.frozen-2020-10-23.yaml
conda activate varfish-db-downloader
pip install -r requirements.txt
This command will download and process all necessary files as well as link all files in a folder to build the final packages.
snakemake
The following variables can be adjusted on the commandline (either export them as variables or preceed the command).
| Variable | Default |
|---|---|
RELEASE_PATH |
releases |
DATA_RELEASE |
current date (YYYYMMDD) |
CLINVAR_RELEASE |
current date (YYYYMMDD) |
JANNOVAR_RELEASE |
current date (YYYYMMDD) |
The output can be found in the folders GRCh37, GRCh38 and releases (default setting).
Use the Makefile to pack the output of the snakemake run to finalize the data release.
make pack_server
make pack_annotator
make pack_jannovar
The following variables can be adjusted on the commandline (either export them as variables, preceed the command or edit directly in the Makefile).
| Variable | Default |
|---|---|
RELEASE_PATH |
releases |
DATA_RELEASE |
current date (YYYYMMDD) |
JANNOVAR_RELEASE |
current date (YYYYMMDD) |
The output can be found in the folder releases:
releases/jannovar-db-YYYYMMDD.tar.gz.sha256
releases/jannovar-db-YYYYMMDD.tar.gz
releases/varfish-annotator-db-YYYYMMDD.tar.gz.sha256
releases/varfish-annotator-db-YYYYMMDD.tar.gz
releases/varfish-server-background-db-YYYYMMDD.tar.gz.sha256
releases/varfish-server-background-db-YYYYMMDD.tar.gz
Information about which VarFish DB Downloader version corresponds to which data release version and can be used with which VarFish Server version:
| VarFish DB Downloader | Data Release | VarFish Server |
|---|---|---|
| v0.2 | 20201006 | <= v0.22.1 |