Skip to content

Latest commit

 

History

History
38 lines (26 loc) · 1.35 KB

README_docker.md

File metadata and controls

38 lines (26 loc) · 1.35 KB
Raw

docker-MSP

This is a docker container for the annotation of genomes and simulation of metagenome datasets.

Usage

  1. Get Docker build files

     git clone https://github.com/CAMI-challenge/MetagenomeSimulationPipeline.git
 git checkout docker

  2. Build the Docker image

     docker build -t="pehofmann/emsep" ./

  3. Create the folders to mount

  4. Run Docker container

     sudo docker run \
 -v /data/cami/test/docker/unittest_MSP/nobackup/tmp:/bbx/mnt/tmp/ \
 -v /data/cami/test/docker/unittest_MSP/nobackup/output:/bbx/mnt/output/ \
 -v /data/cami/test/docker/unittest_MSP/unittest_ga/input:/bbx/mnt/input:ro \
 -v /data/cami/test/docker/unittest_MSP/unittest_ga/ref:/bbx/mnt/ref/:ro \
 -i -t --rm pehofmann/emsep --shell

 sudo docker run \
 -v /data/cami/test/docker/unittest_MSP/nobackup/tmp:/bbx/mnt/tmp/ \
 -v /data/cami/test/docker/unittest_MSP/nobackup/output:/bbx/mnt/output/ \
 -v /data/cami/test/docker/unittest_MSP/unittest_ms/input:/bbx/mnt/input:ro \
 -v /data/cami/test/docker/unittest_MSP/unittest_ga/ref:/bbx/mnt/ref/:ro \
 -i -t --rm pehofmann/emsep --shell

python /opt/tools/MetagenomeSimulationPipeline/genomeannotation.py /bbx/mnt/input/config.cfg python /opt/tools/MetagenomeSimulationPipeline/metagenomesimulation.py /bbx/mnt/input/config.cfg