How to run seqsender with Compose

Source: vignettes/compose_installation.Rmd

SOFTWARE REQUIREMENTS:

  • Linux (64-bit) or Mac OS X (64-bit)
  • Git version 2.25.1 or later
  • Docker version 20.10.14 or later
  • Docker Compose version 2.21 or later
  • Standard utilities: curl, tar, unzip

ADDITIONAL REQUIREMENTS:

See PRE-REQUISITES and REQUIREMENT FILES before proceeding to the next steps

(1) Clone seqsender repo to your $HOME directory 

cd $HOME
git clone https://github.com/CDCgov/seqsender.git
cd seqsender

Here is a quick look of the docker-compose.yaml file:

version: "3.9"

x-data-volumes:
  &data-volume
  type: bind
  source: $HOME
  target: /data

services:
  seqsender: 
    container_name: seqsender
    image: cdcgov/seqsender-dev:latest
    restart: always
    volumes: 
      - *data-volume
    command: tail -f /dev/null

NOTE: source is the storage location of your local machine. This location will be mapped to /data directory inside the container. Here we are mounting the local $HOME directory to /data inside the container.

(3) Start up the seqsender container 

docker-compose up -d

-d: run the container in detached mode

For more information about the docker-compose syntax, see docker-compose up reference

(4) Check if the container is running 

docker container ps


CONTAINER ID   IMAGE                COMMAND        CREATED         STATUS        PORTS      NAMES
b37b6b19c4e8   seqsender:latest     "/bin/bash"    5 hours ago     Up 5 hours               seqsender

(5) See a list of commands in seqsender container 

docker exec -it seqsender bash seqsender-kickoff --help

-t: allocate a pseudo-tty
-i: keep STDIN open even if not attached
-h, --help: show help messages and exit

usage: seqsender.py [-h]
                    {prep,submit,check_submission_status,template,version} ...

Automate the process of batch uploading consensus sequences and metadata to
databases of your choices

positional arguments:
  {prep,submit,check_submission_status,template,version}

optional arguments:
  -h, --help            show this help message and exit

Rather than hastily jump in and submit a production submission right away, we can utilize GISAID’s and NCBI’s “TEST-SERVER” to upload a test submission first. That way submitter can familiarize themselves with the submission process prior to make a real submission.

Note: Duplicate test submissions will result in an error. Please create new sequence names each time you plan to run test submissions to avoid this issue.

Submit a test submission with a pre-processed dataset

Submit a test submission with your own dataset




Any questions or issues? Please report them on our Github issue tracker.