QIIME 2 2017.6 release is now live!


(Matthew Ryan Dillon) #1

The QIIME 2 2017.6 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 2017.6 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!

With the success of the QIIME 2 Forum, we are transitioning away from Slack as a public communication tool. We will remove all general user accounts from Slack when we release QIIME 2 2017.7 (scheduled for mid to late July), so please make sure to export/backup anything you think you might need before then. Moving forward, we encourage users to search for help on the forum, and if a post addressing their question is not found, they can ask a new question. For developers, we recommend using either the forum or an appropriate GitHub issue tracker. We will continue to utilize Slack internally to coordinate releases, dev meetings, etc. with maintainers of plugins in the QIIME 2 GitHub organization.

Here’s the highlights of the release:

  • QIIME 2 framework
  • Methods and visualizers are no longer required to accept at least one input artifact, making it possible to develop actions that do not require artifacts as input.
  • Empty metadata (i.e. metadata without any rows) is now disallowed.
  • Added qiime2.Metadata.merge method for merging one or more Metadata objects using an inner join. Source artifacts are tracked on merged metadata to preserve provenance (source artifacts can be accessed with Metadata.artifacts property).
  • Added PluginManager.importable_formats property for determining which file/directory formats are importable into QIIME 2 artifacts.
  • When using the Artifact API, an action’s (i.e. method or visualizer) docstring now includes the action’s short and long descriptions. Additionally, the inputs and outputs are annotated with the corresponding QIIME 2 types. These can be viewed within IPython by calling ? on an action.
  • Added a new utility for plugin developers to prevent cross-device linking errors.
  • Fixed a bug related to optional parameters. This only affected interface/SDK developers.
  • q2cli
  • qiime tools import has a new --show-importable-formats option that displays the file/directory formats that can be supplied to --source-format to import data into an artifact.
  • Specifying options (inputs, outputs, or parameters) multiple times is now prevented (this previously would discard all but the last declaration). Metadata-specific parameters do allow multiple declarations, to support Metadata merging.
  • Now supports merging Metadata by providing --m-<name>-file options multiple times with different files (including metadata files and artifacts).
  • q2studio
  • The available importable semantic types and formats are now listed with an autocomplete-dropdown when importing.
  • Added UI support for optional parameters (this fixes a bug related to q2-emperor).
  • Fixed a bug that required the first column of a sample metadata mapping TSV to have the label #SampleID.
  • q2studio is now bundled with the QIIME 2 VirtualBox image!
  • q2-feature-classifier
  • Added custom ChunkedHashingVectorizer as a workaround for an upstream issue in sklearn.
  • q2-feature-table
  • Added an --exclude-ids option to filter-samples and filter-features to exclude (instead of retain) samples/features selected by metadata or where parameters.
  • summarize now treats a sampling depth of 0 as “no rarefaction” in the “Interactive Sample Detail” tab of the visualization.
  • q2-types
  • The following semantic types are now viewable as QIIME 2 Metadata:
    • PCoAResults
    • FeatureData[Taxonomy]
    • FeatureData[Sequence]
    • FeatureData[AlignedSequence]
  • Fixed a potential bug related to cross-device linking errors. If you had problems with this in the past, please let us know!
  • q2-dada2
  • Fixed a potential bug related to cross-device linking errors. If you had problems with this in the past, please let us know!
  • Passing 0 to trunc_len/trunc_len_f/trunc_len_r will disable truncation and length-based filtering. This is not generally recommended, but may be necessary for certain highly variable datasets.
  • view.qiime2.org
    • Provenance visualization now renders Metadata nodes (including their provenance, if the supplied Metadata was an Artifact).
    • Page UI has been improved substantially, there is now a gallery and Dropbox links are explicitly supported.
    • An about section now exists with troubleshooting and file hosting requirements.
    • A bug was fixed that prevented edges from being drawn in the provenance tab if the same artifact was provided multiple times as input to the same action. Prior to this fix, only one edge would be drawn for that artifact, now multiple edges are superimposed.
  • q2-deblur
  • Fixed a bug that prevented users from running visualize_stats.
  • q2-metadata
    • This is a new member to the QIIME 2 lineup! This plugin will house metadata-specific actions and currently provides a tabulate visualizer for interacting with metadata (including sorting, filtering, and exporting). See the new QIIME 2 metadata tutorial for examples.
  • q2-demux
  • The summarize quality plot now supports sequences of different lengths. A warning is displayed to the user in this case.
  • docs
  • Added a tutorial for working with QIIME 2 metadata, including examples of the new metadata-related features included in this release.
  • Updated the site logo!
  • Removed references to Slack (see the note above in the general announcement text for motivation).
  • Virtual Machines
    • The VirtualBox build now includes an experimental preview of q2studio! Thanks for making this happen @patrickrosenthal!

Happy QIIME-ing!

Dada2 variable sequence length
Multiple input files
(Evan Bolyen) #40

(Evan Bolyen) #41

(Evan Bolyen) #42

Demux summarize issue
Exporting alpha diversity results into R
Plugin error from deblur
(Evan Bolyen) #43

An off-topic reply has been split into a new topic: Problem upgrading to 2017.6

Please keep replies on-topic in the future.