SPYNE

Command line interface (CLI) for running MIRA (an interactive dashboard for Influenza and SARS-COV-2 Spike-Gene Genome Assembly and Curation) using a Snakemake workflow.

1. Run spyne locally

(i) Clone this respitory

git clone https://github.com/CDCgov/spyne.git

(ii) Navigate to spyne folder

cd spyne

(iii) Check out single_spyne_container branch

git checkout single_spyne_container 

(iv) Run the spyne workflows

NOTE: In the spyne directory, there is a MIRA.sh file that would execute the spyne workflows.

bash MIRA.sh -s {path to samplesheet.csv} -r <run_id> -e <experiment_type> <OPTIONAL: -p amplicon_library> <OPTIONAL: -c CLEANUP-FOOTPRINT> <OPTIONAL: -n> 

Experiment type options: Flu-ONT, SC2-Spike-Only-ONT, Flu_Illumina, SC2-Whole-Genome-ONT, SC2-Whole-Genome-Illumina, RSV-illumina, RSV-ONT
Primer Schema options for SC2: articv3, articv4, articv4.1, articv5.3.2, qiagen, swift, swift_211206
Primer Schema options for RSV: RSV_CDC_8amplicon_230901, dong_et_al

2. Run spyne with Docker

Requirements

• Git version >= 2.21.0
• Docker version >= 18

(i) Clone this respitory

git clone https://github.com/CDCgov/spyne.git

(ii) Navigate to spyne folder

cd spyne

(iii) Check out single_spyne_container branch

git checkout single_spyne_container 

(iv) Build the spyne image

NOTE: In the spyne directory, there is a Dockerfile that contains a list of instructions on how to build and run the spyne container.

docker build -t spyne:latest .

-t: add a tag to an image such as the version of the application, e.g. spyne:v1.0.0 or spyne:latest
.: current working directory of where the Dockerfile is stored

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

docker images

REPOSITORY      TAG        IMAGE ID        CREATED        SIZE
spyne           latest     2c22887402d3    2 hours ago    1.98GB

(v) Run the spyne container

docker run -v /path/to/data:/data --name spyne -t -d spyne:latest

NOTE:

• Change /path/to/data to your local directory where it contains all data files needed to feed into the spyne workflows. This directory is mounted to /data directory inside the container.
  

-t: allocate a pseudo-tty
-d: run the container in detached mode
-v: mount code base and 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 spyne workflows.
--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    spyne:latest    "bash"         5 hours ago     Up 5 hours               spyne

(vi) Execute the spyne workflows inside the container

docker exec -w /data spyne bash MIRA.sh -s {path to samplesheet.csv} -r <run_id> -e <experiment_type> <OPTIONAL: -p amplicon_library> <OPTIONAL: -c CLEANUP-FOOTPRINT>

-w: working directory inside the container. DEFAULT: /data.
Experiment type options: Flu-ONT, SC2-Spike-Only-ONT, Flu_Illumina, SC2-Whole-Genome-ONT, SC2-Whole-Genome-Illumina, RSV-illumina, RSV-ONT
Primer Schema options for SC2: articv3, articv4, articv4.1, articv5.3.2, qiagen, swift, swift_211206
Primer Schema options for RSV: RSV_CDC_8amplicon_230901, dong_et_al

3. Run spyne with Compose

Requirements

• Git version >= 2.21.0
• Docker version >= 18
• Docker Compose Version >= 1.29

(i) Clone spyne repo

git clone https://github.com/CDCgov/spyne.git

(ii) Navigate to spyne folder

cd spyne

(iii) Check out single_spyne_container branch

git checkout single_spyne_container 

(iv) Edit docker-compose.yml file in the spyne folder to link the data inputs, irma, and dais-ribosome images to run the spyne container

version: "3.9"

x-irma-image:
  &irma-image
  irma_image: cdcgov/irma-dev:rsv-support

x-dais-image:
  &dais-image
  dais_image: cdcgov/dais-ribosome:v1.5.4

x-data-volume:
  &data-volume
  type: bind
  source: /home/snu3/irma-testings/rsv-support/FLU_SC2_SEQUENCING
  target: /data

services:
  spyne: 
    container_name: spyne
    image: spyne:latest
    build:
      context: .
      dockerfile: Dockerfile
      args:
        << : [*irma-image, *dais-image]
    restart: always
    volumes:
      - *data-volume
    command: tail -f /dev/null

(v) Start up the spyne 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

(vi) How to run the spyne container

docker exec -w /data spyne bash MIRA.sh -s {path to samplesheet.csv} -r <run_id> -e <experiment_type> <OPTIONAL: -p amplicon_library> <OPTIONAL: -c CLEANUP-FOOTPRINT> 

Experiment type options: Flu-ONT, SC2-Spike-Only-ONT, Flu_Illumina, SC2-Whole-Genome-ONT, SC2-Whole-Genome-Illumina, RSV-illumina, RSV-ONT
Primer Schema options for SC2: articv3, articv4, articv4.1, articv5.3.2, qiagen, swift, swift_211206
Primer Schema options for RSV: RSV_CDC_8amplicon_230901, dong_et_al

4. Push Docker Images to a Registry

You can push docker images to a public registry of choices (e.g. DockerHub, Quay, AWS ECR, etc.). Here, we will authenticate and push spyne image to cdcgov DockerHub account.

(i) Authenticate and log into your DockerHub account

docker login --username <your_username> --password-stdin

--password-stdin: provide a password through STDIN. Using STDIN prevents the password from ending up in the shell's history, or log-files.

(ii) Create another tag for your image. Make sure the tag has your or your organization's account associated with it (e.g., cdcgov). This is useful if you want to tag your image with a latest tag and then another with a specific version of the image.

docker tag spyne:latest cdcgov/spyne:latest

Here, spyne:latest is the local image that you just built, and cdcgov/spyne:latest is an alias image of spyne:latest but with cdcgov account attached.

(iii) See a new list of available images

docker images

REPOSITORY      TAG         IMAGE ID        CREATED        SIZE
spyne           latest      d9e2578d2211    2 weeks ago    1.98GB
cdcgov/spyne    latest      d9e2578d2211    2 weeks ago    1.98GB

(iv) Finally, push cdcgov/spyne:latest image to cdcgov DockerHub

docker image push cdcgov/spyne:latest

Click Here to see a list of available images of spyne on the cdcgov Dockerhub account.

Any questions or issues? Please report them on our github issues