QIIME 2 2017.7 release is now live!


(Matthew Ryan Dillon) #1

The QIIME 2 2017.7 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 2017.7 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!

Moving forward, 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).

We recommend checking out q2-gneiss, a new plugin added in this release that supports novel methods for differential abundance testing. A draft tutorial for q2-gneiss is now available on the QIIME 2 forum. The plugin q2-composition has been removed from QIIME 2 as part of this release (this plugin included the ANCOM method). We had initially removed the q2-composition plugin in favor q2-gneiss in this release, but due to popular demand we have brought q2-composition back. A revised q2-composition tutorial is now provided on the QIIME 2 forum.

Here’s the highlights of the release:

  • QIIME 2’s homepage has been completely redesigned!
  • @Yong-Xin_Liu has been working on a community translation of the QIIME 2 documents! Thanks @Yong-Xin_Liu! :tada:
  • QIIME 2 framework
    • Comments and blank lines are now supported in the QIIME 2 metadata file format, along with backwards-compatible support for QIIME 1 mapping files (where the header is a comment).
    • Optional input artifacts are now supported. They must have a default value of None (similar to optional parameters).
    • There is no longer a required ordering for method/visualization parameters beyond what Python 3 requires. Interfaces are still free to make any decision about ordering they wish. This should only impact plugin developers.
    • qiime2.core.typing.Signature.defaults has been removed in favor of using the ParameterSpec objects. This should only impact interface developers.
    • Action docstrings now match the numpydoc standard. This provides the equivalent of --help to the Artifact API when users of the Jupyter ecosystem use the ? command.
  • docs
    • The importing tutorial now clarifies that .fastq files may be provided for the “fastq manifest” formats in addition to .fastq.gz files.
    • The QIIME 2 Native Installation document now features interactive platform-specific instructions.
    • The QIIME 2 Studio interface document includes more explicit instructions for installation.
    • Clarified AWS upgrade instructions.
    • Fixed outdated even sampling depth suggestion in the Moving Pictures tutorial.
    • Minor typo fixes in the Moving Pictures tutorial.
    • Clarified some requirements on the metadata format in the Metadata tutorial.
  • q2-alignment
    • Added support for running mafft with multiple threads.
  • q2-demux
    • Fixed a bug which would show only the first segment of sample IDs that had an underscore in the summarize visualization.
  • q2-dada2
    • Fixed a bug which prevented trunc_len of 0 from actually being used in denoise-single and denoise-paired.
    • Improved clarity of error message when an error occurs in the R DADA2 scripts invoked by q2-dada2.
  • q2-feature-table
    • Methods rarefy and relative-frequency no longer create feature tables with the uniform-sampling property (see related note below on q2-diversity for details).
  • q2-feature-classifier
    • Removed the num-threads parameter from classify-consensus-blast as it had no effect with the mode that blastn is invoked in (i.e. with a subject provided).
  • q2-diversity
    • Added an --exclude-ids option to filter-distance-matrix to exclude (instead of retain) samples selected by metadata or where parameters.
    • Fixed a bug in the alpha-correlation plots that caused x-axis tickmarks to behave poorly.
    • Single quotes are now properly escaped in alpha-group-significance visualizations. Previously, metadata values containing single quotes would cause the visualization to break.
    • Methods alpha, alpha-phylogenetic, beta, and beta-phylogenetic no longer require the input FeatureTable[Frequency] to have the uniform-sampling property. This requirement excluded non-uniform sampling effort feature tables. It is desirable to support these types of feature tables in certain cases when downstream multivariate statistical analyses account for uniform sampling effort.
  • q2-taxa
    • Removed qiime taxa tabulate in favor of qiime metadata tabulate (see the metadata tutorial for examples).
    • Added the ability to export a CSV of the data from the barplot visualization.
    • The barplot visualization now has scroll bars on the barplot and the legend.
    • The barplot visualization’s legend and barplot can now be downloaded as svg individually.
    • The barplot visualization no longer has a tooltip, instead that information is displayed in a fixed location at the top of the barplot.
  • q2-gneiss
    • This new plugin provides a new set of compositionally aware statistical techniques using balances. This includes different clustering algorithms, visualizations and regression statistics to identify differentially abundant feature partitions. Thanks @mortonjt for putting this plugin together! :tada:
    • Dropped q2-composition in favor of this plugin (the method add-psuedocount was ported to q2-gneiss).
  • q2studio
    • Fixed a regression that allowed actions to be run without specifying an output file (we didn’t actually want this to happen).
    • Fixed a bug that prevent the listing of plugins from showing up in alphabetical order.
  • q2-types
    • Comments and blank lines are now supported in “per-sample sequence” manifest formats, including sniffers and transformers.
    • Duplicate samples are now additionally detected and disallowed in “relative path” manifest formats (previously this validation only happened in the “absolute path” manifest formats).
    • Error messages reported by transformers are both more precise and accurate regarding the “per-sample” formats.
    • Refactored sniffer and transformer code to reduce redundancy and perform consistent validation and parsing in all sniffers/transformers regarding the “per-sample” formats.
    • Added unit tests, increased coverage to 100% for “per-sample sequence” formats, and made existing unit tests and test data more robust.
  • Miscellaneous
    • Enhancements to QIIME 2 developer tools to ensure consistency across QIIME 2 packages (e.g. licensing, required packages, etc.) and to streamline interactive visualization development.

Happy QIIME-ing! :sun_with_face:

(Matthew Ryan Dillon) #28

The QIIME 2 2017.7 Virtual Machines are now live! :tada: