QIIME 2 2017.4 release is now live!


(Jai Ram Rideout) #1

The QIIME 2 2017.4 release is now live! There are lots of exciting new changes packed into this release, and we anticipate having monthly releases moving forward while we are in alpha development. Since this is alpha development software, we highly recommend staying up-to-date with the latest releases. We will only provide support for the latest monthly release of QIIME 2 while in alpha development.

Check out the QIIME 2 2017.4 docs for details on installing or upgrading/updating your QIIME 2 release, as well as tutorials and other resources. Get in touch on the QIIME 2 forum if you run into any issues!

Here’s the highlights of the release:

  • CI/CD system (AKA “busywork”)
  • There is a new Concourse-based continuous integration / continous deployment (CI/CD) system for the QIIME 2 project. It is responsible for automating QIIME 2 releases; creating, testing, and deploying QIIME 2 conda builds and core distributions on any upstream source code change; and other “busywork” tasks.
  • The CI/CD system was a major time investment over the past release cycle. However, it will enable us to spend less time on “busywork” tasks and more time on developing exciting new QIIME 2 features! :smile: It also makes it possible for us to release on a monthly schedule during alpha development.
  • One immediate benefit to QIIME 2 contributors is the ability to quickly and easily set up / bootstrap a complete QIIME 2 development environment. See the .travis.yml files in any of the qiime2 GitHub organization repositories for examples; we’ll have docs on this topic in the future.
  • We will publish a link to the CI/CD system once it has been stress-tested and is ready for public viewing/access. Visitors will be able to see project build logs (e.g. similar to Travis-CI) and other diagnostics.
  • QIIME 2 docs
  • New tutorial on exporting data from QIIME 2 artifacts/visualizations.
  • Expanded examples in filtering data tutorial.
  • Expanded examples in importing data tutorial. This includes a new file format which allows you to map sample IDs to sample sequence data irrespective of file naming conventions.
  • Installing QIIME 2 is even easier now that the latest version of DADA2 is conda-installable. No need to install DADA2 manually through Bioconductor anymore! :beers:
  • The plugin developer guide no longer uses the QIIME 2 plugin cookiecutter template. q2-dummy-plugin has also been decommissioned as its only purpose was to be used with the cookiecutter template. These repositories are now in the qiime2-graveyard organization. :ghost:
  • q2-demux plugin
  • summarize visualizer has a new interactive visualization for exploring single- or paired-end sequence data quality scores. This interactive visualization is intended to replace q2-dada2’s plot-qualities visualization and is a more general-purpose tool for understanding sequence quality scores. q2-dada2’s plot-qualities visualization is scheduled for removal in the next release (2017.5) in favor of q2-demux’s summarize visualization. Thanks for the new viz @jakereps!
  • q2-feature-classifier plugin
  • Added two new methods classify-consensus-blast and classify-consensus-vsearch for BLAST and VSEARCH-based consensus taxonomy classification. Thanks @nbokulich for these new methods!
  • Method classify has been renamed to classify-sklearn.
  • Method fit-classifier has been renamed to fit-classifier-sklearn.
  • Method classify-sklearn has a new read-orientation parameter for correcting the orientation of input reads relative to the reference sequences used to train the classifier. By default, input read orientation is auto-detected and corrected if necessary.
  • Plugins q2-deblur and q2-quality-filter are now part of the QIIME 2 Core 2017.4 Distribution and included in the Moving Pictures tutorial. Thanks @wasade for these new plugins!
  • q2-diversity plugin
  • beta-group-significance visualizer has new pairwise option for performing pairwise statistical tests (this option is off by default).
  • Added new beta-correlation visualizer for performing Mantel tests between an input distance matrix and a Euclidean distance matrix computed from numeric sample metadata categories.
  • q2-dada2 plugin
  • denoise-single and denoise-paired methods have two new chimera-filtering options: chimera_methods and min_fold_parent_over_abundance.
  • q2-phylogeny plugin
  • fasttree method now handles tip identifiers with underscores correctly.
  • QIIME 2 framework
  • qiime2.plugin.Plugin now supports short and long plugin descriptions (short_description and description, respectively). The QIIME 2 plugin docs and q2cli also support displaying these plugin descriptions. Thanks for this new feature @maxvonhippel!
  • qiime2.sdk.PluginManager now has an importable_types property for discovering semantic types that can be used to import data.
  • q2cli
  • qiime tools view for macOS no longer expects a DISPLAY environment variable.
  • The CLI now understands ranged parameters.
  • q2-feature-table plugin
  • Minor UI tweaks and improvements to summarize visualizer.
  • @thermokarst crafted a beautiful QIIME 2 cross stitch for the lab :art:

Happy QIIME-ing!

(Jai Ram Rideout) #2

An off-topic reply has been split into a new topic: Why did q2-dummy-types move to the graveyard?

Please keep replies on-topic in the future.