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docker for JAX Addiction Course 2015
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Short Course On The Genetics Of Addiction

This is a directory for 2-hour bioinformatic workshop on Short Course On The Genetics Of Addiction (August 27, 2015) at The Jackson Laboratory that includes the following tutorials:

The participants use their web browsers to connect to customized Docker containers hosted on Digital Ocean virtual machines (see screen captures below).

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Docker is a lightweight container virtualization platform. We created two Docker images for this course: simecek/addictioncourse2015 (RStudio, DOQTL, DESeq2) and kbchoi/asesuite (kallisto, EMASE). You can run docker containers on your computer or in the cloud environments like AWS, Digital Ocean, Microsoft Azure or Google Cloud. Dockerfile can be also used as a list of instructions how to install the software on your computer.

How to start Digital Ocean droplet?

Here, I will give a description how our virtual machines have been created. You can either create a machine manually on Digital Ocean, SSH to it and start the docker containers. Or you can use R/analogsea package to start a droplet from a command line.

In both cases, first, create an account on Digital Ocean. You should get $10 promotional credit that currently corresponds to free 3.5 days of 8GB machine running expense.

For beginners - create a virtual machine manually

  • Log into your Digital Ocean account. Click on "Create Droplet" button. Choose any droplet hostname and select its size - 8GB memory, 4 CPU, $0.119/hour.

Scroll down to "Select image", click on 'Applications' tab and select Docker. Click on "Create Droplet" button. Droplet now starts in 1-2 minutes. You should receive an email with a password.

  • Note down your droplet's IP.ADDRESS. SSH into your droplet (ssh root@DROPLET.IP.ADDRESS) and pull docker images
    docker pull rocker/hadleyverse
    docker pull simecek/addictioncourse2015
    docker pull kbchoi/asesuite
    
  • Next, download required datasets (~30 minutes)
    mkdir -p /sanger
    chmod --recursive 755 /sanger
    wget --directory-prefix=/sanger ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi
    wget --directory-prefix=/sanger ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz
    mkdir -p /kbdata
    chmod --recursive 755 /kbdata
    wget --directory-prefix=/kbdata ftp://ftp.jax.org/kb/individualized.transcriptome.fa.gz
    wget --directory-prefix=/kbdata ftp://ftp.jax.org/kb/rawreads.fastq.gz
    
  • Finally, run docker containers. If you want to link it to your own data folder like /mydata then use additional -v option like -v /mydata:/mydata
    docker run -d -v /sanger:/sanger -p 8787:8787 -e USER=rstudio -e PASSWORD=rstudio simecek/addictioncourse2015
    docker run -dt -v /sanger:/sanger -v /kbdata:/kbdata -p 8080:8080 kbchoi/asesuite
    

For advanced users - create a virtual machine with R/analogsea package

Access your virtual machine in the web browser

In your browser you can now access RStudio at http://DROPLET.IP.ADDRESS:8787 (user: rstudio, password: rstudio) and the terminal at http://DROPLET.IP.ADDRESS:8080 (user: root, password: root).

You are paying for your Digital Ocean machine as long as it is running. Do not forget to destroy it when you are done!

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simecek
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