frankyan/gatk-tutorial repository overview

⁠Description of GATK-tutorial Docker Image

⁠1. Operating System

Ubuntu 16.04, based on Ubuntu image in Docker store⁠

docker pull ubuntu

⁠2. Software Installed

According to the requriments of the tutorial, add all the necessary softwares and some useful tools to the base Ubuntu image.

• JDK⁠: version 1.8.0_144
• bwa⁠: version 0.7.15
• samtools⁠: version 1.6
• GATK⁠: version 3.8
• picard⁠: version 2.13.2
• Build essential (apt-get)
• Utility tools (apt-get): perl, python, vim, nano, less, ssh, wget, curl, zcat, tar, gunzip, tabix, bgzip, bzip2, gnu-parallel, et. al.

⁠3. Datasets

Two versions of images were built. The differences between the two images are datasets. The pure version only contains all the required softwares and tools. The latest version is based on the pure version but added all the datasets needed in tutorial.

• frankyan/gatk-tutorial:pure : 654 MB
• frankyan/gatk-tutorial:latest : 5 GB

The data in latest version image cost more than 4 GB storage. If it's hard to pull such large image from DockerHub, you can try to pull the much smaller pure image and download those data by yourself. Following is the description of all the data.

⁠Reference Data

All the reference data are part of GATK hg19 resource bundle downloaded from FTP server of Broad Institute. You can check detail information of the resource bundle on GATK webpage⁠. You can directly download hg19 resource bundle from: ftp://ftp.broadinstitute.org/bundle/hg19/ The data are all stored in directory /refData. In latest image, a soft link to the /refData directory has been created in the ~/ home directory of user account student.

• Reference sequence: ucsc.hg19.fasta.gz
• dbSNP in VCF
  • dbSNP 138: dbsnp_138.hg19.vcf.gz
  • dbSNP 138 excluding the impact of the 1000 Genomes project: dbsnp_138.hg19.excluding_sites_after_129.vcf.gz
• Gold standard indels from Mills' study⁠ and Phase 1 of 1000G project⁠: Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz
• Indels from Phase 1 of 1000G project⁠: 1000G_phase1.indels.hg19.sites.vcf.gz

⁠Experimental Sequencing Data

A pair-end sequencing reads data will be used in the tutorial. The data are stored in directory /seqData. And a soft link to the /seqData directory has been created in the ~/ home directory of user account student.

• S555_03B_CHG024155-Lane1-3016021772-TACCCTGC_L007_R1.fastq.gz
• S555_03B_CHG024156-Lane2-3016021772-TACCCTGC_L008_R2.fastq.gz

⁠Container Usage

⁠1. Install Docker and Pull Image

Tips: If you are in China, you can try to use a mirror server in China for pulling image. Use this command for pulling: docker pull registry.docker-cn.com/frankyan/gatk-tutorial

• macOS and win10 Pro (or Enterprise) users

  It's easy to install Docker CE (Community Edition)⁠ on updated macOS and win10 Pro.

  • Download Docker CE for MacOS⁠
  • Download Docker CE for Windows 10 Professional or Enterprise⁠ After installation, open terminal (macOS) or PowerShell(windows) or cmd (windows), then type in the following command to pull the GATK-tutorial image from Docker Hub to your own computer.

  docker pull frankyan/gatk-tutorial
  

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  For pure version image, use command docker pull frankyan/gatk-tutorial:pure

• win10 Home or previous windows version users

  Windows 10 Home or previous edition cannot run docker directly based on HyperV tech, so you have to install the docker-toolbox⁠ based on VirtualBox tech.

  • Download Docker-toolbox for Windows 10 Home or previous versions⁠ After installation, you need to open a PowerShell(windows) or cmd (windows) and run the following command lines to set environment of docker.

  docker-machine create default
  @FOR /f "tokens=*" %i IN ('docker-machine env --shell cmd') DO @%i
  

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  Then use command line docker pull frankyan/gatk-tutorial or docker pull frankyan/gatk-tutorial:pure to pull the full or pure image.

You can use command docker images to list all the pulled local images.

By the way, you can install some other termial emulator for much better experience. You can try iTerm2⁠ in mac OS, or cmder⁠ in windows PC.

⁠2. Initialize a Container and Log in

⁠2.1 Initialization

docker run -it --name gatk frankyan/gatk-tutorial

This command will initialize a running container named as 'gatk' and then you have already logged in a tty of the linux system as user 'student'. Have fun! Press key ctrl+p then ctrl+q to log out.

⁠2.2 Log in and out

• Check container status (running or stopped): docker ps -a
• If the 'gatk' container was stopped, start it before logging in : docker start gatk
• Log in : docker exec -it gatk bash
• Log in as root : docker exec -it --user root gatk bash
• Log out : Press key ctrl+p then ctrl+q to log out.

⁠2.3 Remove

Only when you finished the tutorial course and want to release hard driver space, you can remove the container and image.

• Remove container : docker rm -f gatk
• Remove image: docker rmi -f frankyan/gatk-tutorial

⁠3. Tips for Docker-toolbox Users

For docker-toolbox users, you must run following command lines when you open a new terminal.

docker-machine start default
@FOR /f "tokens=*" %i IN ('docker-machine env --shell cmd') DO @%i

⁠References:

• https://docs.docker.com/⁠
• https://yeasy.gitbooks.io/docker_practice/content/container/run.html⁠