# Install Docker # Please follow the instructions at https://docs.docker.com/install/ # or try the local install with rpm packages wget -c https://ref-db.edgebioinformatics.org/EDGE/Docker/docker-ce-dependencies-rpms-for-centos.tgz tar xvzf docker-ce-dependencies-rpms-for-centos.tgz sudo yum localinstall *rpm # Download the docker images wget -c https://ref-db.edgebioinformatics.org/EDGE/Docker/edge_24_1_ubuntu18_20231115.tar.gz wget -c https://ref-db.edgebioinformatics.org/EDGE/Docker/edge_ubuntu_mysql_docker.tgz # Import Docker saved image docker load < edge_24_1_ubuntu18_20231115.tar.gz docker load < edge_ubuntu_mysql_docker.tgz # Download EDGE database from web server You will need >500GB disk space for all databases ## Pipeline database is ~17Gb and contains the other databases needed for EDGE wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_pipeline_databases.tgz ## BWA index is ~41Gb and contains the databases for bwa taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_bwa_index.tgz ## HOST genomes BWA index is ~41Gb for Host removal, including human, bacteria, phiX, viruses, invertebrate vectors of human pathogens wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_HostIndex.tgz ## NCBI Genomes is ~21Gb and contain the full genomes for prokaryotes and some viruses wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_NCBI_genomes.tgz ## GOTTCHA database is ~16Gb and contains the custom databases for the GOTTCHA taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_GOTTCHA_db.tgz ## NT database is ~25Gb and contains the NCBI nt database for contig identification wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_nt_20160426.tgz ## ShortBRED database is ~27Mb and contains the databases used by ShortBRED for virulence factors and read based antibiotic resistance analysis wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_ShortBRED_Database.tgz ## Diamond database is ~16Gb and contains the databases from RefSeq for protein based taxonomic identification wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_diamond_db.tgz ## MetaPhlAn4 database is 14Gb file contains the databases used for the MetaPhlAn4 taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_metaphlan4DB.tgz ## GOTTCHA2 databases is 38Gb file and contains the custom databases for the GOTTCHA2 taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_GOTTCHA2_db_20190729.tgz ## Kraken2 database is 39Gb file contains the databases used for the Kraken2 taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_Kraken2_db_20211216.tgz ## Centrifuge database is 20G file contains the databases used for the Centrifuge taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_Centrifuge_db_20200329.tgz ## PanGIA database is 35G file for PanGIA taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_PanGIA_db.tgz ## MICCR database is 48GB contains the databases used for the contig taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_ContigTax_db_20190114.tgz ## CheckM database is 275MB contains the databases used for the Metagenome Binned contig quality assessment. wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_checkM_db_20190213.tgz ## Qiime2 database is 1.4GB contains 16s,18s and ITS db. wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_qiime2_db_20230719.tgz ## AntiSmash database is 3.2GB contains pfam resfam tigrfam can clusterblast db for antismash version 6 wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_AntiSmash6.tgz (Optional) ## Other Host bwa index ~18Gb for host removal, including pig, sheep, cow, monkey, hamster. and goat. wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_otherHostIndex.tgz ## For machine with < 32Gb memory, we suggest to use the smaller BWA index (~14Gb) and contains the databases for bwa taxonomic identification pipeline wget -c https://ref-db.edgebioinformatics.org/EDGE/dev/edge_dev_bwa_mini_index.tgz # Decompressed each tar.gz file (tar -xzvf) for being used later # Usage $ docker create --name mysql_data --volume /var/lib/mysql bioedge/edge_ubuntu_mysql $ docker run -d --privileged=true --security-opt "seccomp:unconfined" \ --cap-add=SYS_ADMIN --cap-add=SYS_PTRACE \ --volumes-from mysql_data \ -v /path/to/database:/home/edge/database \ -v /path/to/EDGE_output:/home/edge/EDGE_output \ -v /path/to/EDGE_input:/home/edge/EDGE_input \ -v /path/to/EDGE_report:/home/edge/EDGE_report \ -p 80:80 -p 8080:8080 --name edge bioedge/edge_24_1_ubuntu18:20231115 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/database:/home/edge/database mounts the databse obtained from the above download step. * The -v /path/to/EDGE_input://home/edge/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://home/edge/EDGE_output mounts the EDGE output directory to persist the output files in the host. * The -v /path/to/EDGE_report:/home/edge/EDGE_report mounts the EDGE report directory to persist the report 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: admin_docker@my.edge/Admin1234! * For security, you may need update the credentials if the server will be used by others or public. ### Note * This image is built on top of offical Ubuntu 18.04.2 LTS Base Image, and is officially supported on Docker Engine version 18.09.2. * The user management can be accessed by http://localhost:8080/userManagement if host port is 8080 ### Commands for checking status and error log * Check the mariadb status in container: $ docker exec edge service mysql status where "edge" is the container name when user `docker run` it with --name flag * And user management system service status: $ docker exec edge service tomcat7 status * For the Apache web server status and log: $ docker exec edge service apache2 status $ docker exec edge tail /var/log/apache2/error.log $ docker exec edge tail /var/log/apache2/access.log ### Citation Po-E Li, Chien-Chi Lo, Joseph J. Anderson, Karen W. Davenport, Kimberly A. Bishop-Lilly, Yan Xu, Sanaa Ahmed, Shihai Feng, Vishwesh P. Mokashi, Patrick S.G. Chain; Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Nucleic Acids Research, Volume 45, Issue 1, 9 January 2017, Pages 67–80, https://doi.org/10.1093/nar/gkw1027 ### Contact Info Chien-Chi Lo: Paul Li: