CGPS Core-FP

Identifies core genes from a sequence and compares them to a reference. The core is used for building trees.

Create a core profile

docker run -i --rm -v <FULL_PATH_TO_SEQENCE>:/data registry.gitlab.com/cgps/cgps-core-fp:<VERSION> query /data/<SEQUENCE_NAME>

For example:

seq="../wgsa_data/saureus/example.fasta"
docker run -i -v $(cd $(dirname $seq) && pwd)/$(basename $seq):/data/$(basename $seq) registry.gitlab.com/cgps/cgps-core-fp:latest query /data/$(basename $seq) > $(basename $seq '.fasta').core.json

Run the tests

npm test

Building the databases outside of the image

docker run -it --rm -v $(pwd):/data -w /data --entrypoint bash registry.gitlab.com/cgps/cgps-core-fp:latest build.sh

Creating the images for production

Run the build-images.sh script:

./build-images.sh v2.0.2