QIIME 2 2017.8 release is now live!


(Matthew Ryan Dillon) #1

The QIIME 2 2017.8 release is now live! There are lots of exciting new changes packed into this release that are described below. Through the end of 2017 we will have monthly releases. We highly recommend staying up-to-date with the latest releases to get access to new features, bug fixes, documentation, etc. We will only provide user support for the latest monthly release of QIIME 2 as these monthly releases continue through the end of 2017.

QIIME 2 will succeed QIIME 1 on January 1, 2018. QIIME 1 will no longer be supported at that time, as development and support effort for QIIME will be focused entirely on QIIME 2. We recommend that existing QIIME users begin transitioning from QIIME 1 to QIIME 2 now.

Check out the QIIME 2 2017.8 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!

We will provide official conda builds on release day. Virtual machine builds such as AWS and Docker will be released within the following week. We will post a follow-up announcement here when those builds become available.

Here’s the highlights of the release:

  • QIIME 2 Framework
    • Added validation to Metadata and MetadataCategory to disallow empty/null IDs or column labels. Also added type-checking of inputs to constructors.
  • docs
    • Added a differential-abundance testing with q2-gneiss tutorial. This tutorial was ported from a community tutorial written by @mortonjt.
    • The ANCOM section of the moving pictures tutorial has been re-added and reformulated to meet the assumptions of ANCOM better.
    • Removed the “upgrading/updating” page from the install docs as it was causing confusion with users, and the page isn’t necessary until we provide longer-running releases with patches. To upgrade/update to the latest version of QIIME 2, follow the install instructions appropriate for your computing environment.
    • Added a tip to the native install docs about running conda clean when troubleshooting installation issues.
  • q2-sample-classifier
    • This new plugin supports machine learning prediction of sample data - check out the new tutorial to learn how it works!
  • q2-longitudinal
    • This new plugin supports statistical and visual comparisons of longitudinal study designs and paired samples - check out the new tutorial to learn how it works!
  • q2-feature-table
    • Added a new core-features visualizer for identifying features that are shared among some user-defined fraction of samples. This visualizer is analogous to QIIME 1’s compute_core_microbiome.py script.
    • Added a new group method for grouping samples or features in a feature-table based on values in a metadata category. This method is analogous to QIIME 1’s collapse_samples.py script.
    • The merge method now allows basic handling of overlapping axes. Currently you can either allow for overlapping samples, or overlapping features, but not both. We will expand this in the future to support other overlapping methods.
    • Fixed a bug that prevented users from being able to download their sequences from the tabulate-seqs visualization when viewing at view.qiime2.org.
  • q2-diversity
    • A new visualizer alpha-rarefaction was added which allows you to view an alpha-diversity metric as a rarefaction curve alongside sample metadata for a given range of sampling depths. Thanks for this new visualizer @Max_von_Hippel! :tada:
    • Added new beta-rarefaction visualizer, which provides a heatmap showing the correlation between beta diversity distance matrices computed by repeatedly rarefying at a given sampling depth. Thanks for this new visualizer @Kleptobismol! :tada:
    • beta, beta-phylogenetic, and core-metrics now have an n-jobs parameter to turn on parallelism (default is no parallelism).
  • q2-taxa
    • Fixed a bug where changing the default color scheme would not update colors in the legend.
  • q2-gneiss
    • Fixed a bug in dendrogram-heatmap when there are tree tips that are not present in the feature table.
    • Fixed a bug in dendrogram-heatmap and gradient-clustering when there are samples in the metadata that are not present in the feature table.
  • q2-alignment
    • Fixed a bug where MAFFT would truncate very long sequence IDs (~250 characters in length). This was a problem for users who chose not to hash their sequence IDs during denoising (or otherwise imported them, e.g. from running DADA2 in R).
  • q2view
    • Fixed a bug that caused q2view to become extremely unresponsive in Firefox 55.
    • Fixed a bug that cause a Protocol Violation error in Firefox 55 when following a link in a fresh session.
    • Links to files with an unknown extension how default to a download dialog.
  • q2-feature-classifier
    • Updated plugin to work with scikit-learn 0.19.0 and later.
  • q2cli
    • The debug log’s filepath (printed when an error is encountered) no longer has a trailing period, making it easier to copy.
  • q2templates
    • Plugin developers: if you’re using DataFrame.to_html in your code, you might want to check this out! Added q2templates.df_to_html function, which wraps DataFrame.to_html to avoid truncation of cell contents in the output HTML. Default pandas behavior is to truncate cell contents that exceed 50 characters. The function also uses different default parameters than DataFrame.to_html to give uniform styling to HTML tables that are compatible with q2template themes. These defaults can be overridden.
  • q2-types
    • Removed q2_types.per_sample_sequences.PerSampleDNAIterators and q2_types.per_sample_sequences.PerSamplePairedDNAIterators view types, along with their corresponding transformers. We discovered that these view types never actually worked and weren’t being used anywhere, so this change shouldn’t affect users or plugin/interface developers.
  • Miscellaneous
    • Various enhancements to QIIME 2 developer tools to ensure consistency across QIIME 2 packages and to streamline development.

Happy QIIME-ing!

QIIME 2 Project Status
Dada2 back to qiime 2
(Jai Ram Rideout) #24

(Matthew Ryan Dillon) #25

The QIIME 2 Virtual Machines are now available! We have QIIME 2 2017.8 available on AWS, Docker, and VirtualBox, please see the docs for more information. Thanks!

Error in command for generating PCoA plot
(Matthew Ryan Dillon) #26

An off-topic reply has been split into a new topic: Can’t find QIIME 2 2017.8 Virtual Box Image

Please keep replies on-topic in the future.

(Matthew Ryan Dillon) #27

An off-topic reply has been split into a new topic: Upgrading to QIIME 2 2017.8

Please keep replies on-topic in the future.