Docker-dedup-hic

Data-type-independent, generic bam sorting module

• Input : a readID-sorted bam file (.bam)
• Output : a readID-sorted bam file with duplicate flags ('d' or 0x400) (.dedup.bam)

This repo contains the source files for a docker image stored in duplexa/dedup-hic:v1. (we will change the docker hub account soon)

Cloning the repo

git clone https://github.com/4dn-dcic/docker-dedup-hic
cd docker-dedup-hic

Resources tools

Major software tools used inside the docker container are downloaded by the script downloads.sh. This script also creates a symlink to a version-independent folder for each software tool. In order to build an updated docker image with a new version of the tools, ideally only downloads.sh should be modified, but not Dockerfile, unless the new tool requires a specific APT tool that need to be downloaded. The downloads.sh file also contains comment lines that specifies the name and version of individual software tools.

Building docker image

You need docker daemon to rebuild the docker image. If you want to push it to a different docker repo, replace duplexa/dedup-hic:v1 with your desired docker repo name. You need permission to push to duplexa/dedup-hic:v1.

docker build -t duplexa/dedup-hic:v1 .
docker push duplexa/dedup-hic:v1

Usage

Run the following in the container.

run.sh <input_bam> <output_prefix>
# input_bam : a readID-sorted bam file
# output_prefix : prefix of the output bam file.