How to run seqsender with Docker

Source: vignettes/docker_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
  • 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
docker build -t seqsender:latest .

-t: add a tag to an image, e.g. seqsender:1.0.0 or seqsender:latest

(3) After the build is completed, you can check if the image is built successfully 

docker images

REPOSITORY    TAG       IMAGE ID        CREATED        SIZE
seqsender     latest    d9e2578d2211    2 weeks ago    581GB

(4) Run seqsender container 

docker run \
-v $HOME:/data \
-t -d seqsender:latest \
--name seqsender

-t: allocate a pseudo-tty
-d: run the container in detached mode
-v: mount data files from host directory to container directory [host_div]:[container_dir]. By exposing the host directory to docker container, docker will be able to access data files within that mounted directory and use it to fire up the seqsenderworkflows. NOTE: Here we are mounting the local $HOME directory to /data directory inside the container.
--name: give an identity to the container

For more information about the Docker syntax, see Docker run reference

To check if the container is built successfully

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.