Sign inSign up

etheleon/metaomicsgraphdb

By etheleon

•Updated almost 9 years ago

An executable to generate neo4j graphDB for omics analyses.

Image
0

892

etheleon/metaomicsgraphdb repository overview

DOI

⁠Graph Data Model

workflow

⁠Setup DB (wo Docker)

Clone the repository.

$ git clone --recursive [email protected]:etheleon/omics.git

Batch import data into single <database.db> file.

$ ./configure -d=contig -d=metabolism -d=taxonomy -t=10 \
    -x=$HOME/db/taxonomy \
    -j=$HOME/local/neo4j-community-2.2.2/bin/neo4j-import \
    -c=$HOME/contigs \
    -ftp --user=<keggFTP username> --password=<keggFTP password>

Edit org.neo4j.server.database.location=/graph/db to org.neo4j.server.database.location=</path2/meta4j/out/database/database.db> in neo4j-server.properties.

⁠Dependencies

SoftwareVersion / Packages / etc
Perl> 5.10
R> v3.1.2 is required and the following packages (dplyr igraph XML magrittr)
neo4j2.2.3 (JAVA; JAVA_HOME has to be defined in your $HOME/.bashrc else NEO4J-import will not work

⁠External datasets

  • NCBI taxonomy (download on your own)
  • KEGG FTP (optional)

⁠Setup DB (with Docker)

⁠Running the DB (Docker)

You'll need to have Docker⁠ installed.

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

Database needs to be mounted, make sure you have the following folder structure. where graph.db is the output

/projectFolder
└── graph.db
    ├── bad.log
    ├── index
    ├── messages.log
    ├── neostore
    ├── neostore.counts.db.a
    ├── neostore.counts.db.b
    ├── neostore.id
    ├── neostore.labeltokenstore.db
    ├── neostore.labeltokenstore.db.id
    ├── neostore.labeltokenstore.db.names
    ├── neostore.labeltokenstore.db.names.id
    ├── neostore.nodestore.db
    ├── neostore.nodestore.db.id
    ├── neostore.nodestore.db.labels
    ├── neostore.nodestore.db.labels.id
    ├── neostore.propertystore.db
    ├── neostore.propertystore.db.arrays
    ├── neostore.propertystore.db.arrays.id
    ├── neostore.propertystore.db.id
    ├── neostore.propertystore.db.index
    ├── neostore.propertystore.db.index.id
    ├── neostore.propertystore.db.index.keys
    ├── neostore.propertystore.db.index.keys.id
    ├── neostore.propertystore.db.strings
    ├── neostore.propertystore.db.strings.id
    ├── neostore.relationshipgroupstore.db
    ├── neostore.relationshipgroupstore.db.id
    ├── neostore.relationshipstore.db
    ├── neostore.relationshipstore.db.id
    ├── neostore.relationshiptypestore.db
    ├── neostore.relationshiptypestore.db.id
    ├── neostore.relationshiptypestore.db.names
    ├── neostore.relationshiptypestore.db.names.id
    ├── neostore.schemastore.db
    ├── neostore.schemastore.db.id
    ├── neostore.transaction.db.21
    ├── neostore.transaction.db.22
    ├── neostore.transaction.db.23
    ├── neostore.transaction.db.24
    ├── neostore.transaction.db.25
    ├── neostore.transaction.db.26
    ├── neostore.transaction.db.27
    ├── rrd
    ├── schema
    └── store_lock

After starting the container navigate to 127.0.0.1:7474 on your machine's browser

login in

Tag summary

Content type

Image

Digest

Size

791.3 MB

Last updated

almost 9 years ago

docker pull etheleon/metaomicsgraphdb