Zika bioinformatics pipeline

Run scripts via Docker. Notes on building and pushing Docker image are here.

Run

Data volume

Create a named data volume that mirrors local MinION data/ to data/ within container:

docker create --name zibra-data -v /Volumes/Meristem/data:/data zibra/zibra

This is to get MinION data into the Docker container. Note that the path to local directory has to be an absolute path. Change /Volumes/Meristem/data to wherever local data is stored. Notes on data schema are here.

Samples volume

Create a named data volume that mirrors local sample metadata samples/ to samples/ within container:

docker create --name zibra-samples -v /Volumes/Meristem/samples:/samples zibra/zibra

This is to get sample metadata into the Docker container. Note that the path to local directory has to be an absolute path. Change /Volumes/Meristem/samples to wherever local data is stored. Notes on metadata schema are here

Build volume

Create a named data volume that mirrors local build/ to build/ within container:

docker create --name zibra-build -v /Volumes/Meristem/build:/build zibra/zibra

This is to get data out of the Docker container. Note that the path to local directory has to be an absolute path. Change /Volumes/Meristem/build to wherever local results are stored.

Start

Enter docker image:

docker run -t -i --volumes-from zibra-data --volumes-from zibra-samples --volumes-from zibra-build zibra/zibra /bin/bash

Run script:

python scripts/pipeline.py