Public | Automated Build

Last pushed: a month ago
Short Description
Automated build of the ZiBRA pipeline. More details at zibraproject.org.
Full Description

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
Docker Pull Command
Owner
zibra
Source Repository

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