The QIIME 2 2019.1 release is now live! This release mostly focused on upgrading project dependencies, updating to Python 3.6, a new r-vegan Adonis visualizer, and as always, minor bug fixes. Thanks to everyone involved for their hard work!
As a reminder, our next planned QIIME 2 release is scheduled for late April 2019 (QIIME 2 2019.4), but please stay tuned. We are planning on quarterly releases in 2019. Right now, the next proposed releases look like:
- QIIME 2 2019.4
- QIIME 2 2019.7
- QIIME 2 2019.10
Check out the QIIME 2 2019.1 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 2 if you run into any issues!
Virtual machine builds (and new pre-trained classifiers) are available right now!
Here’s the highlights of the release:
-
QIIME 2 Framework
-
@turanoo fixed a bug in
Metadata.__repr__that cause minor explosions in some edge cases.
- QIIME 2 now requires a minimum version of Python 3.6 to run — this is handled for you automatically when installing via one of our “official” methods, so no need to worry! Check out this post to learn more about the motivation and rationale for this change.
- QIIME 2 environments now run on the latest versions of scipy, numpy, pandas, and matplotlib!
Now that’s what I call fresh!
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@turanoo fixed a bug in
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docs
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@gregcaporaso updated the Atacama tutorial’s paper reference.
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@gregcaporaso updated the Atacama tutorial’s paper reference.
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Library
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@raptorace27, @J1411, tanman987, and jbell-97 teamed up to fix a bug when adding or editing plugins that didn’t check to see if the current editor was also listed as a plugin author. This was important because plugin permissions (in terms of being able to edit the plugin listing) are tied directly to “authorship,” so it was possible for a user to “lock themselves out” of their own plugin! Yikes!
-
@raptorace27, @J1411, tanman987, and jbell-97 teamed up to fix a bug when adding or editing plugins that didn’t check to see if the current editor was also listed as a plugin author. This was important because plugin permissions (in terms of being able to edit the plugin listing) are tied directly to “authorship,” so it was possible for a user to “lock themselves out” of their own plugin! Yikes!
-
q2cli
- Corrected cross-device link error when using
qiime tools exportto convert an artifact to a single file. (This most commonly occurred when/tmpwas on a different file system than where the exported file’s destination was.)
- Corrected cross-device link error when using
-
q2-longitudinal
- Updated the plugin citation to reflect the final publication status.
-
q2-types
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FeatureTables can now be used as metadata in QIIME 2 actions that consume metadata objects. Make sure you are inputting a table that is in the correct orientation! The default orientation of FeatureTables enable their use as sample metadata. Use the newtransposeaction (see below) to use feature tables as feature metadata. Thanks @Nicholas_Bokulich!
-
@thermokarst updated the validator used for ensuring
AlphaDiversityFormatfiles are well-behaved. This format now returns a clear error message when it runs into trouble (rather than just throwing its hands up in frustration
).
-
-
q2-feature-classifier
- Both
classify-consensus-*methods now have aquery_covparameter to optionally filter alignment results by query coverage.
- Both
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q2-feature-table
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@turanoo added a new method (
transpose), which allows you to transpose the rows and columns of aFeatureTable[Frequency]!
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@turanoo added a new method (
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q2-gneiss
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@mortonjt fixed a bug in
ilr-phylogeneticwhere mismatched tables and trees would raise an error.
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@mortonjt fixed a bug in
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q2-diversity
- @thermokarst fixed a bug that caused the number of available cores to be incorrectly detected in certain environments, which caused a spurious error in a few methods.
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@Nicholas_Bokulich added a new visualizer,
adonis, that wraps the adonis function from the Vegan R package. This visualizer performs adonis (a.k.a. PERMANOVA) tests. Unlike thebeta-group-significanceaction, adonis can perform multi-way PERMANOVA tests, and can operate on numeric variables. It does not generate plots or perform pairwise tests, so thebeta-group-significanceaction is still the best method for one-way PERMANOVA tests.
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q2-metadata
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@Claudia_Coronel fixed a UI bug in
tabulate, the rendered table now more clearly indicates which column sort widget belongs to which column label.
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@Claudia_Coronel fixed a UI bug in
- Related Projects
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iTOL
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Added support for QZAs of
FeatureData[AlignedSequence]. When dropped onto iTOL trees, these will automatically create a multiple sequence alignment dataset. Note that the display of alignments in iTOL is not supported in circular or unrooted modes.
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Added support for QZAs of
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iTOL
Happy QIIME-ing! 