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docker-nsm-tools

A collection of tools used by the nsm-pipelines

All tools are installed in /usr/local/bin/ and all jar files are placed in /usr/local/jars/

How to use the image

Run a tool command in the container (samtools in this case):

docker run bruggerk/nms-tools:latest samtools

give nsm-tools access to reference data in read-only mode, here as /references

docker run -v [PATH-TO-REFERENCE-DATA]:/references/:ro bruggerk/nsm-tools:latest samtools

However as the majority of the tools needs, and generates, data you will need to make a directory available through volumes:

# This will run docker mounting your current working directory in /run, and execute the program in /run
docker run -v [PATH-TO-REFERENCE-DATA]:/references/:ro -v`pwd`:/run/ -w /run bruggerk/nsm-tools:latest samtools

Tools in container :

  • samtools
  • bcftools
  • tabix
  • bwa
  • gatk
  • verifyBamID
  • bedtools
  • minimap
  • salmon

Jars in container :

  • picard