QIIME 2 2019.1 release is now live!

release

(Q2-D2) #1

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. :balloon:
    • 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! :lemon: Now that’s what I call fresh!
  • docs
    • @gregcaporaso updated the Atacama tutorial’s paper reference. :open_book:
  • Library
    • @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! :lock: :lock_with_ink_pen:
  • q2cli
    • Corrected cross-device link error when using qiime tools export to convert an artifact to a single file. (This most commonly occurred when /tmp was on a different file system than where the exported file’s destination was.)
  • q2-longitudinal
    • Updated the plugin citation to reflect the final publication status.
  • q2-types
    • 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 new transpose action (see below) to use feature tables as feature metadata. Thanks @Nicholas_Bokulich! :ice_cream:
    • @thermokarst updated the validator used for ensuring AlphaDiversityFormat files 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 :raised_hands:).
  • q2-feature-classifier
    • Both classify-consensus-* methods now have a query_cov parameter to optionally filter alignment results by query coverage.
  • q2-feature-table
    • @turanoo added a new method (transpose), which allows you to transpose the rows and columns of a FeatureTable[Frequency]! :cake:
  • q2-gneiss
    • @mortonjt fixed a bug in ilr-phylogenetic where mismatched tables and trees would raise an error.
  • 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.
    • @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 the beta-group-significance action, adonis can perform multi-way PERMANOVA tests, and can operate on numeric variables. It does not generate plots or perform pairwise tests, so the beta-group-significance action is still the best method for one-way PERMANOVA tests.
  • q2-metadata
    • @Claudia_Coronel fixed a UI bug in tabulate, the rendered table now more clearly indicates which column sort widget belongs to which column label. :circus_tent:
  • Related Projects
    • iTOL
      • 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.

Happy QIIME-ing! :sun_with_face:


[Preview] QIIME 2 2019.1 development changelog
(Evan Bolyen) pinned globally #2

(Didit) #3

I hope in this new version, we can use dada2 plugins with less time than before… but I see dada2 still has no update yet in qiime 2… hmmm…lets see… I need filtering/denoising/trimming function that real good with less uptime… Thanks for the efforts qiime 2 team.


(Meha) #4

Hello, I would like to know how can I upgrade/ update my last Qiime2 Version to 2019.1 version? And must be my last Qiime2 version updated to new one or not necessary?
Thank you


#5

Hi, you can just install new release, and you will have two separate versions of Qiime, after it you can delete one of them. Also you can check changelog and decide if you need to update. But it is better to have a latest version, since developers are working hard to fix problems and add new features.


(Meha) #6

Good idea. Thanks for the quick reply. I am a new Linux user. If it is possible, please tell me how can omit the old version on my Linux (Ubuntu)? Is there some commands or what. If so, please let me know what related commands are there.


(Justine) #7

Hi @Mehrdad,

If you’re using conda and doing a native installation, just follow the install directions, using a new name (i.e. qiime2-2019-01).

Best,
Justine


#8

Run in the terminal
conda env remove -n qiime2-2018.11
Of course you should specify version you want to remove.
Good luck in your analysis


(benjamin w.) #9

Thanks QIIME2 team, happy new year. Ben


(Kris Budd) #10

Is anyone having trouble with speed on this new update? I’m running same machine same memory etc. but a script that took maybe a few hours on the 2018 version is taking DAYS to run on this new update?


(Evan Bolyen) #11

Just to double check, are you running with the same dataset or new data?


(Kris Budd) #12

Same Data just re-running DeBlur with a new trim length. Previously it only took a few hours now its been running since Friday


(Evan Bolyen) #13

That is very strange, would you be able to open a new topic with more details and cc @wasade on it? This sounds like something we should explore further.


(benjamin w.) #14

No issues with speed, however, we transitioned to a new HPC core and the folks who run it have installed several versions. I can try to run it through different versions to benchmark. The HPC core at our research center is super fast, it actually runs DADA2 and Deblur in a quarter of the time.


(Matthew Ryan Dillon) #15

Cross-reference to the detailed discussion: 2019.1 vs 2018.11 Speed