semenleyn/refprep_pipeline repository overview

⁠RefPrep docker image

Docker image with tools for running a reference genome preparation for the variant calling pipeline.

⁠Content

• BWA
• Picard (to run Picard use java -jar /usr/local/bin/picard.jar command)
• Samtools
• MUMmer
• JRE
• BLAST
• ISfinder balst database (IS database in the /root/data/blast_db folder)
• Perl
  • JSON module
• Python3
  • Pandas
  • Biopython

⁠Build

Build using Buildx module: Docker Buildx⁠. The build is using multi-stage build setup: Use multi-stage builds⁠.

docker buildx create --name mybuilder
docker buildx use mybuilder
docker buildx build --platform=linux/amd64,linux/arm64 -t semenleyn/refprep_pipeline:latest --push .