/spyne

Primary LanguagePython

output: html_document: keep_md: yes

Requirements

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

Steps to run spyne container

(1) Clone this respitory

git clone https://github.com/cdcgov/spyne/tree/container_init

(2) CD to spyne folder

(3) Check out container_init branch

git checkout container_init

(4) Pull down irma and dais-ribosome images

  • From a docker registry

  IRMA: docker pull public.ecr.aws/n3z8t4o2/irma:1.0.2p3
  Dias-Ribosome: docker pull public.ecr.aws/n3z8t4o2/dais-ribosome:1.2.1

(5) Run irma and dais-ribosome containers

  IRMA: docker run -v /path/to/data:/data --name irma:1.0.2p3 -t -d public.ecr.aws/n3z8t4o2/irma:1.0.2p3
  Dais-Ribosome: docker run -v /path/to/data:/data --name dais-ribosome:1.2.1 -t -d public.ecr.aws/n3z8t4o2/dais-ribosome:1.2.1

NOTE:

  • Change /path/to/data to your local directory where it contains all data files needed to feed into the IRMA and Dais-ribosome workflow. This directory is mounted to /data directory inside the container.

(6) Build spyne image and run its container

NOTE: In the SC2-seq-spike directory, there is a Dockerfile that contains a list of instructions and steps of how to build and run the spyne workflow.

A. Build the development version

  • Using a build-arg
docker build -t spyne-dev:v1.0.0 --build-arg BUILD_STAGE=dev .
  • Using a specific dockerfile for development stage (e.g. Dockerfile.dev)
docker build -t spyne-dev:v1.0.0 -f Dockerfile.dev .

-t: add a tag to an image such as the version of the application, e.g. spyne-dev:v1.0.0 or spyne-dev:latest
--file, -f: name of the Dockerfile
--build-arg: set the build time variable for docker image. In this case, we want to build the development stage by setting build variable BUILD_STAGE=dev.

The image took approximately < 10 mins to build

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

docker images

REPOSITORY             TAG        IMAGE ID        CREATED        SIZE
spyne-dev      v1.0.0     2c22887402d3    2 hours ago    1.58GB

To run the spyne-dev container

docker run -v /path/to/data:/data -v /path/to/spyne:/spyne -v /var/run/docker.sock:/var/run/docker.sock --name spyne-dev-1.0.0 -t -d spyne-dev:v1.0.0

NOTE:

  • Change /path/to/data to your local directory where it contains all data files needed to feed into the spyne workflow. This directory is mounted to /data directory inside the container.
  • Change /path/to/spyne to your local spyne directory. This directory must contain all of the code base needed to build the spyne workflow.
  • /var/run/docker.sock:/var/run/docker.sock is used to connect the host's docker.socket to container's docker.socket where you can run a container inside of another 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 workflow.
--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-dev:v1.0.0     "bash"         5 hours ago     Up 5 hours               spyne-dev-1.0.0

B. Build the production version

  • By default
docker build -t spyne-prod:v1.0.0 .
  • Using a specific dockerfile for production stage (e.g. Dockerfile.prod)
docker build -t spyne-prod:v1.0.0 -f Dockerfile.prod .

-t: add a tag to an image such as the version of the application, e.g. spyne-prod:v1.0.0 or spyne-prod:latest
--file, -f: name of the Dockerfile

The image took approximately < 10 mins to build

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

docker images

REPOSITORY             TAG        IMAGE ID        CREATED        SIZE
spyne-prod     v1.0.0     c436f88dcd2f    2 hours ago    1.58GB

To run the spyne-prod container

docker run -v /path/to/data:/data -v /var/run/docker.sock:/var/run/docker.sock --name spyne-prod-1.0.0 -t -d spyne-prod:v1.0.0

NOTE:

  • Change /path/to/data to your local directory where it contains all data files needed to feed into the spyne workflow. This directory is mounted to /data directory inside the container.
  • /var/run/docker.sock:/var/run/docker.sock is used to connect the host's docker.socket to container's docker.socket where you can run a container inside of another 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 workflow.
--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
475741fd9bc7   spyne-prod:v1.0.0    "bash"      5 hours ago    Up 5 hours               spyne-prod-1.0.0

(7) To execute snakemake pipeline inside spyne-prod-1.0.0 container

docker exec -w /data spyne-prod-1.0.0 bash snake-kickoff <path/to/samplesheet.csv> <runpath> <experiment_type>

(8) To execute irma pipeline inside irma-1.0.2p3 container

  • FOR PAIRED-END
docker exec -w /data irma-1.0.2p3 IRMA <MODULE|MODULE-CONFIG> <R1.fastq.gz|R1.fastq> <R2.fastq.gz|R2.fastq> [path/to/]<sample_name>
  • For SINGLE-END
docker exec -w /data irma-1.0.2p3 IRMA <MODULE|MODULE-CONFIG> <fastq|fastq.gz> [path/to/]<sample_name>

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