QIIME 2 Core Distribution Builds


(Matthew Ryan Dillon) #1

QIIME 2 Core Distribution Builds

We are pleased to announce the release of several new core distribution builds for QIIME 2! If you are interested in experimenting with QIIME 2 these options can get you from zero to QIIME 2 in no time! We currently support the QIIME 2 2.0.6 release cycle, including all of the core plugins, in the following formats:

  • Amazon Web Services EC2 AMI Images
  • Virtualbox VMDK Images
  • Docker Images

The core plugins included are:

  • alignment
  • composition
  • dada2
  • demux
  • diversity
  • emperor
  • feature-classifier
  • feature-table
  • phylogeny
  • taxa
  • types

Virtualbox Quickstart

  1. Set up Virtualbox on your computer (see virtualbox.org for details).
  2. Download the QIIME 2 Core Virtualbox Image here: https://data.qiime2.org/distro/core/qiime206.zip.
  3. Unzip the qiime206.zip file.
  4. Launch VirtualBox, and create a new machine (press the New button)
  5. A new window will show up. Click ‘Next’
  6. In this screen type QIIME 2 Core 2.0.6 as the name for the virtual machine then select Linux as the Operating System, and Ubuntu (64 bit) as the version. Click Next.
  7. Select the amount of RAM (memory). You will need at least 2048 MB, but the best option is based on your machine. After selecting the amount of RAM, click Next.
  8. Select “Use existing hard drive”, and click the folder icon next to the selector (it has a green up arrow). In the new window click ‘Add’, and locate the virtual hard drive that was unzipped in step 3. Click Select and then click Next.
  9. In the new window click Finish.
  10. Launch the virtual machine. When prompted, select the user qiime2, and enter the password qiime2.

Amazon Web Services Quickstart

  1. Set up an Amazon Web Services (AWS) account, and log in.
  2. Set your region to “US West (Oregon)”.
  3. When launching an instance, select “Community AMIs”, and search for “QIIME 2 Core” (the AMI ID is ami-c401aca4).
  4. When prompted to set up a security group, make sure that port 22 is open.
  5. When prompted to set up an SSH keypair, choose “Proceed without a keypair”.
  6. Once the machine has finished booting, you can SSH into the machine using:
$ ssh [email protected]<PUBLIC_AWS_IP_ADDRESS>
# When prompted, provide the password `qiime2`

Docker Quickstart

  1. Set up Docker on your computer (see docker.com for details).
  2. In a terminal with Docker activated, run docker pull qiime2/core:latest.
  3. Run docker run -t -i -v $(pwd):/data qiime2/core qiime to confirm that the image was successfully fetched.

Future distribution builds

At this stage we’re unsure of what types of builds we’ll continue to release in the future. We expect that for at least the next few QIIME 2 releases we’ll provide the three builds included here, but we may ultimately phase out the AWS and VirtualBox builds. This is because our release of these builds restricts users to a specific operating system/cloud platform/etc, so we feel that we may better serve our user community by providing cross-platform builds (e.g., Docker containers) and detailed instructions for how to work with these.


No disk space on virtual box
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(Matthew Ryan Dillon) #2

(Matthew Ryan Dillon) #3

Just a quick follow up regarding the 2.0.6 VirtualBox image — a new build has been released (build number 1484941248). This build includes an increased base disk size (dynamically allocated up to 1 TB). The new build also automatically loads the VirtualBox Guest Additions Installation Disk so that setting up those Additions is as simple as possible (Guest Additions are used for sharing clipboard and directories between guest and host, among other things). If you have the previous build (1479486933), you might want to consider downloading this new version (accessible at the same link as above: https://data.qiime2.org/distro/core/qiime206.zip). You can determine which build you have by checking your VirtualBox Manager window - the build number is part of the default title:

Also, the old build can be accessed here.


No disk space on virtual box