Omics neo4j docker image

This repository provides the instructions for seting up the container environment to run the omics database (NEO4J).

Please install Docker beforehand.

Docker Image

You could choose to build your own image using the provided Dockerfile or pull the image: docker pull etheleon/omics-neo4j-container

Download DB

Download the DBs using the links provided below expires in 1 year in Dec 2018.

Please approach me for the passphrase to decrypt the gz files.

Simulation

1. Initial analysis with Single Copy Gene KOs only

   • Contigs compared with trimmed NR db contigs_against_trimmednr
   • Contigs compared with NR db full NR

2. With all KOs

   • Contigs compared with trimmed NR db trimmed NR
   • Contigs compared with NR db full NR

Ulu Pandan

1. Initial analysis with Single Copy Gene KOs trimmed NR, full NR
2. With all KOs trimmed NR, full NR

Perturbation

Time-series

Decrypt, Decompress

DB=allKOS_fullnr
#decrypt
gpg --yes --batch --passphrase=[Enter your passphrase here] $DB.tar.gz.gpg
#gunzip and untar
tar -zvxf $DB.tar.gz

Run Docker

#Run the Docker container
data=$PWD/$DB
docker run \
    --rm \
    --name omics \
    --publish=7474:7474 --publish=7687:7687 \
    --volume=$data:/data \
    --ulimit=nofile=40000:40000 \
    etheleon/omics-neo4j-container:latest