Docker Image for Apollo annotation reports

This image contains everything needed to generate an Apollo per-user report each day, with rules defined at http://bipaa.genouest.org/.

Using the Container

We highly recommend using a docker-compose.yml to run your containers.

Apollo-report needs to have access to the full genome sequence in fasta format of each genome. If you have access to the directory used by Apollo to store all its jbrowse data, you will want to run it like that:

version: "2"
services:
  report:
    image: quay.io/abretaud/apollo-report:latest
    environment:
        APOLLO_URL: http://apollo:8080/ # Full URL to the Apollo server
        APOLLO_EXT_URL: http://example.org/somewhere/apollo/ # Full URL to the Apollo server, accessible from anywhere (default= APOLLO_URL)
        APOLLO_USER: admin@apollo # Admin account to connect to apollo
        APOLLO_PASS: password # Password to connect to apollo
        ADMIN_USERS: userx@apollo,usery@apollo # Set this to a list of users who will have access to all the data from all users.
        APOLLO_MOUNTPOINT: /apollo-data/
    volumes:
        - ./apollo_data_dir/:/apollo-data/:ro #
        - ./my_annotation_groups.tsv:/data/annotation_groups.tsv:ro # If you have annotation groups, mount the list file on this location
    ports:
      - "3000:80"

Otherwise, you can directly mount fasta files in a specific directory:

version: "2"
services:
  report:
    image: quay.io/abretaud/apollo-report:latest
    environment:
        APOLLO_URL: http://apollo:8080/ # Full URL to the Apollo server
        APOLLO_EXT_URL: http://example.org/somewhere/apollo/ # Full URL to the Apollo server, accessible from anywhere (default= APOLLO_URL)
        APOLLO_USER: admin@apollo # Admin account to connect to apollo
        APOLLO_PASS: password # Password to connect to apollo
        ADMIN_USERS: userx@apollo,usery@apollo # Set this to a list of users who will have access to all the data from all users.
    volumes:
        - ./my_genome.fa:/data/genomes/Genus_species.fa:ro # Always mount the genome fasta files to this location, named by organism common name
        - ./my_other_genome.fa:/data/genomes/Genies_specus.fa:ro # Always mount the genome fasta files to this location, named by organism common name
        - ./my_annotation_groups.tsv:/data/annotation_groups.tsv:ro # If you have annotation groups, mount the list file on this location
    ports:
      - "3000:80"

A cron task is configured to generate the report every day. You can consult the script error log by looking at /var/log/apollo_report.log.

Configuring the Container

The following environment variables are also available:

APOLLO_URL: http://apollo:8080/ # Full URL to the Apollo server, accessible from the container
APOLLO_EXT_URL: http://example.org/somewhere/apollo/ # Full URL to the Apollo server, accessible from anywhere (default= APOLLO_URL)
APOLLO_USER: admin@apollo # Admin account to connect to apollo
APOLLO_PASS: password # Password to connect to apollo
ADMIN_USERS: userx@apollo,usery@apollo # Set this to a list of users who will have access to all the data from all users.
ALL_ADMINS: 0 # Set this to 1 if you want users to have access to other users information (ADMIN_USERS will be ignored)
DETAILED_REPORT: 0 # Set this to 1 if you want to display more detailed information for admin users
ANNOTATION_GROUPS: 1 # Set this to 0 if you don't want to validate AnnotGroup attribute
SPLIT_USERS: 1 # Set this to 0 if you don't want to remove the @something suffix from apollo user names
REPORT_PATH: /data/report/ # Location for report files, no need to change this in most cases
LOCAL_ONLY: for testing purpose only, will not try to contact a remote apollo server, will expect a raw gff extract from apollo to be mounted on /data/raw_apollo.gff, and a genome to be mounted on /data/genome.fa
APOLLO_MOUNTPOINT: path to the mounted Apollo data directory (if mounted)