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Dockerfile
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# How to run Xenomapper in a docker container
# Docker File Author / Maintainer
# MAINTAINER Matthew Wakefield <[email protected]>
# First you will need install docker. On MacOS you do
# brew install Caskroom/cask/virtualbox
# brew install docker
# brew install boot2docker
# boot2docker download
# boot2docker init
# boot2docker up
# $(boot2docker shellinit)
# You then need to create a docker container. In the same directory as this file you type
# docker build -t xenomapper .
# This will run the following executable part of this file
FROM ubuntu:trusty-20190515
MAINTAINER Matthew Wakefield <[email protected]>
RUN apt-get update && apt-get install -y \
samtools \
python3-pip \
git
RUN pip3 install git+https://github.com/genomematt/xenomapper.git
# congratulations - you now have a docker container with xenomapper installed!
# To test it run
# docker run -i xenomapper xenomapper --version
# (note the first xenomapper is the container name, the second the program name)
# To do anything useful with it you will need to mount some data in the container
# The simplest version of this is to mount a directory from the host.
# This must be an absolute path, and something like $HOME/my/data/directory:/data
# will mount your host directory in the container as /data
# docker run -it -v $HOME/repos/xenomapper/xenomapper/tests/data/:/data/ xenomapper xenomapper --primary_sam /data/paired_end_testdata_human.sam --secondary_sam /data/paired_end_testdata_mouse.sam --unresolve /data/docker_unresolved.sam
# Note that you will get the primary_specific on std_out, the read count category summary on std_err and unresolved in a host file $HOME/repos/xenomapper/xenomapper/tests/data/docker_unresolved.sam