QIIME 2 2022.2 is now available!

[q2d2]

The QIIME 2 2022.2 release is now available! Thanks to everyone involved for their hard work!

As a reminder, our next planned QIIME 2 release is scheduled for April, 2022 (QIIME 2 2022.4), but please stay tuned for updates.

Check out the QIIME 2 2022.2 docs for details on installing the latest QIIME 2 release, as well as tutorials and other resources. Get in touch on the QIIME 2 Forum if you run into any issues!

Virtual machine builds will be available sometime this week (except for q2galaxy, its docker container is already published) - watch this topic thread for an update!

New Documentation:

This release is timed with the release of several QIIME 2 documentation projects that provide new ways to learn QIIME 2 now, and a glimpse into where we're headed with QIIME 2 documentation in the future.

• We're excited to share a new multiple interface QIIME 2 tutorial, the Cancer Microbiome Intervention tutorial. This tutorial derives from data from over 12,000 human-cancer-associated microbiome samples published in 2021 in Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Users can choose whether to follow along using the QIIME 2 Galaxy Interface (which you can learn how to install here), the QIIME 2 command line interface, or the Python 3 API. This content is provided as a JupyterBook, a documentation tool that you can expect to see a lot more of around the QIIME 2 ecosystem.
• A new, free QIIME 2 YouTube course that parallels the Cancer Microbiome Intervention tutorial. Over the next several months, we'll release new videos each week. This is our first video tutorial series that focused on the Galaxy interface, so if you want to learn to use QIIME 2 through Galaxy, this is a great place to start! @gregcaporaso provides a 3.5 minute introduction to the course here.
• @gregcaporaso is sharing a preview of his QIIME 2 JupyterBook, q2book. This is a work-in-progress, and not yet complete, but you can find useful background on QIIME 2 archives (i.e., .qza and .qzv files), semantic types, importing, and more topics that will help you deepen your understanding of how QIIME 2 works and why.
• Our Jupyter Book based tutorials (mentioned above), can be found on a new page in our user documentation, titled Jupyter Book Tutorials.

Additional features:

• QIIME 2 Framework
  • @ChrisKeefe made a handful of improvements/tweaks to Usage
  • @ebolyen fixed an inconsistency in the view_type parameter of Usage.import_from_format, both string and classes are accepted as arguments now
  • Artifact API has now been renamed to the Python3 API
• q2cli
  • @ebolyen fixed a bug in the Usage driver which resulted in a namespace collision
  • @ebolyen fixed an issue where the incorrect usage variable was returned for Usage.view_as_metadata
• q2galaxy
  • When installing q2galaxy via the pre-built docker image, the conda environment is now already included. This results in a larger base image, but makes it far less likely that installation will fail. As a result, the first job will no longer take in excess of 40 minutes to complete
  • @ebolyen added a new Usage driver to automatically generate RST instructions for use within Galaxy tools and documentation
  • @ebolyen fixed an issue with string sanitization in the generated tools. (Unusual characters like ; would be silently converted, breaking functionality.)
  • @ebolyen added a new template function to provide an automatically nested and alphabetized tool_conf.xml file. See q2galaxy template tool-conf --help
• q2-sample-classifier
  • @misialq added cross-validation to KNN sample classification based on distance matrices
• q2-dada2
  • @sixvable added support for PacBio CCS data and @Keegan-Evans and @lizgehret added some final tweaks and tests + data. For more details be sure to checkout @benjjneb's DADA2 paper (and datasets!) that this is a wrapper for
• q2-longitudinal
  • @ebolyen added support for automatically quoting formula terms in linear-mixed-effects. Now column names like my-category will be quoted as Q('my-category') instead of raising an error.
• q2-mystery-stew
  • @ebolyen added more sophisticated metadata interactions. Now tests include Usage.view_as_metadata and Usage.merge_metadata

Happy QIIMEing!

[q2d2]

Docker images for q2galaxy are available now. See installation instructions and video.

[q2d2]

Hi folks! The moment you've been waiting for has arrived! QIIME 2 virtual machines are now available!

[ebolyen (Evan Bolyen)]

Minor update:

A few OS-X dependencies were moved around and resulted in conda no longer resolving packages on OS-X. We've update the environment files to reflect the new dependencies and everything seems to be working as expected now. We've also re-solved the dependencies on linux as well to keep things consistent.

If you've been having issues installing this release on OS-X, delete your current environment file (qiime2-2022.2-py38-osx-conda.yml) and start the installation over by downloading the (now-updated) environment file.

If you have not had this issue, then no worries, there's nothing particularly notable about the dependency updates, and we are not aware of any related bugs impacting QIIME 2. This means you don't need to do anything if you already have a working install.

For the curious, here's how the dependencies were updated.

[Roddyjocif (Roddy Jorquera)]

Hi guys, I am having some problems trying to update my VirtualBox to the qiime 2022.2.

When downloading the qiime 2022.2 image following the link "https://data.qiime2.org/distro/core/2022.2" (as recommended at "https://s3-us-west-2.amazonaws.com/qiime2-data/distro/core/virtualbox-images.txt"), I get all I would need to install the previous image, the downloaded file´s name is "QIIME 2 Core - 2021.11 (1638916567)". Maybe an amazon issue? is there any other way to obtain the qiime 2022.2 image for VirtualBox?

Thank you for making all these tools available for all =)
Best regards.
Roddy

[Keegan-Evans]

@Roddyjocif,

We have a patch for the release that we are finishing up this week, as soon as all of the files are ready for it, I will build a new Vbox image and let you know when it is ready!

[Keegan-Evans]

@Roddyjocif,

Just to be clear, there is nothing you were doing wrong, the Virtual Box image that is available is the wrong one, but we will be uploading the correct one soon!

[Roddyjocif (Roddy Jorquera)]

Thanks a million @Keegan-Evans !
Best of lucks.

[lizgehret]

Hi @Roddyjocif,

Thanks for your patience! The new Virtual Box image has just been uploaded, so you should be all set to download that latest image at your convenience. Happy ing!

[q2d2]

Hi all, we have released a few minor patch updates this week for the 2022.2 release.

• QIIME 2 Framework: @ebolyen added support for alternative "missing" metadata schemas. We plan on providing new docs and/or tutorials for this in future releases.
• q2-diversity: @yoshiki exposed the option to subsample with replacement when running the core-metrics-phylogenetic pipeline.
• q2-diversity-lib: @thermokarst fixed a bug introduced in newer versions of unifrac that caused certain diversity metric computations to allocate 100% of the host's CPUs.

Also, as @lizgehret mentioned above, she has prepared all new VMs that include these patches - you can check out the latest AWS, Docker, and VirtualBox images here:

https://docs.qiime2.org/2022.2/install/virtual/

These will be the final AWS and VirtualBox images that the QIIME 2 team provides - we will continue to support conda ("native") and docker installation methods. Thanks!

@q2d2

As a reminder, our next planned QIIME 2 release is scheduled for April, 2022 (QIIME 2 2022.4), but please stay tuned for updates.

Regarding the proposed 2022.4 release - we decided to issue this small patch release in lieu of a full-blown 2022.4 release, and we are still planning on when our next full release will occur, but probably some time in the next ~2 months.

Happy QIIMEing!