chienchilo/bioedge repository overview

⁠EDGE Bioinformatics

This is docker image for version 1.1 of EDGE Bioinformatics, a product of collaboration between Los Alamos National Laboratory and the Naval Medical Research Center sponsored by the Defense Threat Reduction Agency.

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data. The bioinformatics platform allows users to address a wide range of use cases including assay validation and the characterization of novel biological threats, clinical samples, and complex environmental samples.

⁠How to use this image

⁠Install Docker

See Docker at https://www.docker.com/⁠

⁠Obtain the docker image

$ docker pull chienchilo/bioedge

⁠Obtain inital mysql database

$ git clone -b docker https://github.com/LANL-Bioinformatics/EDGE.git

⁠Download EDGE database from ftp server

# Pipeline database is ~7.9Gb and contains the other databases needed for EDGE   
$ wget -c ftp://ftp.lanl.gov/public/genome/EDGE/1.1/edge_pipeline_v1.1.databases.tgz

# GOTTCHA database is ~14Gb and contains the custom databases for the GOTTCHA taxonomic identification pipeline
$ wget -c ftp://ftp.lanl.gov/public/genome/EDGE/1.1/GOTTCHA_db_for_edge_v1.1.tgz

# BWA index is ~41Gb and contains the databases for bwa taxonomic identification pipeline
$ wget -c ftp://ftp.lanl.gov/public/genome/EDGE/1.1/bwa_index1.1.tgz

# NCBI Genomes is ~8Gb and contain the full genomes for prokaryotes and some viruses
$ wget -c ftp://ftp.lanl.gov/public/genome/EDGE/1.1/NCBI_genomes_for_edge_v1.1.tar.gz

# Decompressed each tar.gz file (tar -xzvf) for later use.    

⁠Start EDGE bioinformatics instance

$ docker run -d --cap-add SYS_PTRACE -v /path/to/mysql:/var/lib/mysql -v /path/to/database:/opt/apps/edge/database -v /path/to/EDGE_output:/opt/apps/edge/edge_ui/EDGE_output -v /path/to/EDGE_input:/opt/apps/edge/edge_ui/EDGE_input -p 80:80 -p 8080:8080 --name edge chienchilo/bioedge

Wait for few seconds for the docker image to start EDGE service and Open http://localhost/⁠ on the browser to start experience EDGE.

• The -v /path/to/mysql:/var/lib/mysql part of the command mounts the /my/own/mysql (obtain from the git clone above) directory from the underlying host system as /var/lib/mysql inside the container, where MySQL by default will write its data files. Using this to persist the database data in the host.
• The -v /path/to/database:/opt/apps/edge/database mounts the databse obtained from the above download step.
• The -v /path/to/EDGE_input://opt/apps/edge/edge_ui/EDGE_input mounts the EDGE input directory structure (obtain from the git clone above) to persist the input/upload files/user projects in the host.
• The -v /path/to/EDGE_output://opt/apps/edge/edge_ui/EDGE_output mounts the EDGE output directory to persist the output files in the host.
• The -p host:container bind the host port 80 and 8080 to container port 80 and 8080 inside the container. You can change the 80 and 8080 to fit your host system requirements.

⁠Default credentials

• EDGE user: [email protected]⁠/admin
• MYSQL root: root/admin

⁠Note

• The image size is around 7.3GB.
• This image is built on top of offical Ubuntu 14.04.3 LTS and is officially supported on Docker version 1.8.2.
• A local web service (e.g. Apache) is required for viewing http://localhost/⁠
• The user management can be accessed by http://localhost:8080/userManagement⁠ if host port is 8080
• There is an issue to mount host volume using MAC OSX. https://github.com/boot2docker/boot2docker/issues/581⁠.

⁠Contact Info

Chien-Chi Lo: [email protected]⁠ Paul Li: [email protected]⁠ Anderson, Joseph J. CIV: [email protected]⁠