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ParSNP

This container implements ParSNP from the Harvest suite.

Includes

  • ParSNP: parsnp
  • FastTree: FastTree or fasttree
  • RAxML: raxmlHPC-PTHREADS
  • Mash: mash
  • PhiPack: Phi
  • HarvestTools: harvesttools

Requirements

Running a container

Pull the image from Docker Hub.

docker pull staphb/parsnp:latest

OR, clone this repository to build & test the image yourself.

git clone git@github.com:StaPH-B/docker-builds.git
cd docker-builds/parsnp/1.5.6
# Run tests
docker build --target=test -t parsnp-test .
# Build production image
docker build --target=app -t parsnp .

Example data analysis

Set up some input data.

mkdir -p parsnp/input_dir
cd parsnp/input_dir
wget \
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/698/515/GCA_000698515.1_CFSAN000661_01.0/GCA_000698515.1_CFSAN000661_01.0_genomic.fna.gz \
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/749/005/GCA_000749005.1_CFSAN000669_01.0/GCA_000749005.1_CFSAN000669_01.0_genomic.fna.gz
gunzip *.gz
cd ../

Run the container to generate a core genome alignment, call SNPs, and build a phylogeny. Output files are written to output_dir.

docker run --rm -v $PWD:/data -u $(id -u):$(id -g) staphb/parsnp:latest parsnp \
-d input_dir \
-o outdir_parsnp \
--use-fasttree \
-v \
-c \
-r !