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Download

To be able to build and run the software, we first need to download the scripts and binary files. Additionally to have a fully functioning EVAdb many third-party datasets should also be downloaded. Data from gnomAD, dbSNP and others is used in many filtering steps to find rare variants or variants associated with the given phenotype of the patient. After downloading the scripts and Dockerfiles, we will build the container images.

Are pre-built Docker containers available for EVAdb?

Currently, the Docker containers for EVAdb are not available on a public docker registry. Therefore, the images must be built on a local machine before use.

EVAdb

All files necessary to deploy EVAdb can be found in the git repository of EVAdb (here). The docker branch contains Dockerfiles and docker-compose scripts for building and installing the software.

Proxy

If youre locked behind a restrictive proxy that you need to access the internet from your build host you have to adapt the Dockerfiles. Currently, it is necessary to set the http_proxy and https_proxy environment variables.

# Prefix each Dockerfile with
ENV http_proxy http://<USER>:<PW>@<IP>:<PORT>/
ENV https_proxy http://<USER>:<PW>@<IP>:<PORT>/

RUN git config --global https.proxy ${https_proxy} \
  && git config --global http.proxy ${http_proxy} \
  && git config --global https.proxyAuthMethod basic \
  && git config --global http.proxyAuthMethod basic

To clone the EVAdb docker branch, use

git clone -b docker https://github.com/mri-ihg/EVAdb.git

Third-Party Data

When building the container images and on first startup of the application, it is recommended to have some third party datasets available. It is possible to run the application without this data for development purposes, but in a production setup these datasets should be present in order for all features to work as expected (f.e. gnomAD filtering).

hg19 vs GRCh38

All library file URL's have to be adjusted for hg38

If you intend to process hg38 with the current version of EVAdb, make sure to include the correct library files. All URL's in the table below are for hg19.

Dataset Storage

Some of the datasets are very large. gnomAD genomes for example exceeds 200GB in size. Make sure to have enough disk space available when downloading these assets.

Dataset Description URL
dbNSFP Polyphen2 and SIFT scores are taken from dbNSFP ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv3.5a.zip
CADD Cadd scores https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh37/whole_genome_SNVs.tsv.gz
gnomAD Genome aggregation database Exome and Genome builds https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz
https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz
OMIM Mendelian inheritance in men Request individual acces at omim.org