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