# QIIME 2 2018.8 release is now live!
**URL:** https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860
**Category:** Announcements
**Tags:** release
**Created:** [August 31, 2018, 9:59pm UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860 "2018-08-31T21:59:22Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@q2d2](https://forum.qiime2.org/u/q2d2)
#### Post date: [August 31, 2018, 9:59pm UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/1 "2018-08-31T21:59:22Z")
The QIIME 2 2018.8 release is now live! There are lots of exciting new changes packed into this release that are described below.
Our next planned QIIME 2 release is tentatively scheduled for October(ish) 2018 (QIIME 2 2018.10), but please stay tuned.
Check out the [QIIME 2 2018.8 docs](https://docs.qiime2.org/2018.8/) 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 will be available sometime next week.
* * *
## Hereβs the highlights of the release:
- [QIIME 2 Framework](https://github.com/qiime2/qiime2)
- @ChrisKeefe - When calling docstrings through the Artifact API, arguments now appear in the same order used in the function signature itself, making documentation more intuitive and creating parity with the CLI.
- [docs](https://docs.qiime2.org/2018.8)
- @turanoo - Updated the tutorial docs to reflect the new flags added to `qiime tools (import|export|extract)`.
- @John_Chase - Added metadata example to the Artifact API interface page. π
- @turanoo - Fixed a typo in the OTU Clustering tutorial. β¨
- @ChrisKeefe - Plugin and Action pages in the docs now include import statements to make access more transparent for users of the Artifact API, and copy-buttons for convenience. π
- @turanoo - Modified the Moving Pictures tutorial to reflect the addition of a new pipeline in `q2-phylogeny`.
- @Nicholas_Bokulich - Updated the [`q2-sample-classifier` tutorial](https://docs.qiime2.org/2018.8/tutorials/sample-classifier/) to describe various new methods, changes in outputs, and add FLOWCHARTS! π
- @Nicholas_Bokulich - Updated the `q2-feature-classifier` tutorial to describe requirements that reference sequences and taxonomy should be paired.
- @Nicholas_Bokulich - Updated the diversity analysis flowchart in the overview tutorial to show where feature table subsampling occurs in the `core-metrics*` pipelines.
- @Nicholas_Bokulich - Updated the `q2-longitudinal` tutorial to describe the new actions added to that plugin in this release.
- [@lisa55asil](https://github.com/lisa55asil) - Updated the `gneiss` tutorial
- @colinbrislawn - Added "updating by installing again" instructions to the install docs. β¬
- [q2view](https://view.qiime2.org/)
- @turanoo - Added more examples to the gallery γ½ π
- [q2-diversity](https://docs.qiime2.org/2018.8/plugins/available/diversity/)
- @ChrisKeefe - In 2017, the beta-correlation pipeline was split into two separate functions [distance-matrix](https://docs.qiime2.org/2018.8/plugins/available/metadata/distance-matrix/) and [mantel](https://docs.qiime2.org/2018.8/plugins/available/diversity/mantel/). A new [beta-correlation pipeline](https://github.com/qiime2/q2-diversity/pull/215) recreates the original functionality.
- [@HannesHolste](https://github.com/hannesholste) - Added an approximation method to PCoA to dramatically improve the computational performance for large distance matrices (tens of thousands of samples). A new parameter in `qiime diversity pcoa` lets users specify the number of dimensions you want to compute, by default all dimensions are computed (as in previous versions of QIIME).
- @Yoshiki - Added `qiime diversity pcoa-biplot` to compute PCoA biplots that project a feature table into an ordination space.
- @thermokarst - Fixed a problem in the alpha-rarefaction visualization that prevented scrolling on the legend.
- @mortonjt - Added `aitchison` distance as a new metric to `beta`. This change adds an optional `pseudocount` parameter to the method.
- @yoshiki - Added `permdisp` as a method for `beta-group-significance`.
- @jakereps - Improved error message when metadata is empty as a result of filtering.
- [q2cli](https://docs.qiime2.org/2018.8/interfaces/q2cli/)
- Tab completion is now _automatically_ available after activating your conda environment in bash and ZSH.
- **β Breaking changes in `q2cli` β**
As part of our efforts to keep the builtin commands of `q2cli` consistent we have updated the subcommands available under the `tools` category. The commands impacted are:
- [`qiime tools import`](https://docs.qiime2.org/2018.8/tutorials/importing/)
- [`qiime tools export`](https://docs.qiime2.org/2018.8/tutorials/exporting/#exporting-data)
- [`qiime tools extract`](https://docs.qiime2.org/2018.8/tutorials/exporting/#exporting-versus-extracting)
Please update your workflows accordingly (e.g. scripts, helper commands, etc.).
Details of the changes are presented below:
### `qiime tools import`
#### old:
```bash
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path pe-64-manifest \
--output-path paired-end-demux.qza \
--source-format PairedEndFastqManifestPhred64
```
#### new:
Please note that `--source-format` has been renamed to `--input-format`.
```bash
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path pe-64-manifest \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred6
```
### `qiime tools export`
#### old:
```bash
qiime tools export \
unrooted-tree.qza \
--output-dir exported-tree
```
#### new:
Please note the positional `INPUT` argument has been replaced with an
`--input-path` option, and the `--output-dir` option has been renamed to
`--output-path`.
```bash
qiime tools export \
--input-path unrooted-tree.qza \
--output-path exported-tree
```
### `qiime tools extract`
#### old:
```bash
qiime tools extract \
feature-table.qza \
--output-dir extracted-feature-table
```
#### new:
Please note the positional `INPUT` argument has been replaced with an
`--input-path` option, and the `--output-dir` option has been renamed to
`--output-path`.
```bash
qiime tools extract \
--input-path feature-table.qza
--output-path extracted-feature-table
```
Thanks @turanoo!
- @turanoo - `qiime tools export ` now supports exporting a file or a directory into another [format](https://github.com/qiime2/q2cli/pull/189). π
- @turanoo - Built-ins now support printing a [success message](https://github.com/qiime2/q2cli/issues/184) after completion of a command. π₯¨ π
- [q2-quality-control](https://docs.qiime2.org/2018.8/plugins/available/quality-control/)
- @Nicholas_Bokulich - fixed a bug where the TAR and TDR values were transposed in `evaluate-composition`. See [this post](https://forum.qiime2.org/t/incorrect-results-produced-by-q2-quality-control-evaluate-composition/4784) for more details.
- [q2-sample-classifier](https://docs.qiime2.org/2018.8/plugins/available/sample-classifier/)
- @Nicholas_Bokulich - Added two new visualizers β `scatterplot` and `confusion-matrix` β to plot accuracy results from regressors and classifiers, respectively.
- @Nicholas_Bokulich - Random splitting into training/test data is now performed on the metadata, not on the feature table. Effect on users: faster, lower memory, more efficient splitting!
- @Nicholas_Bokulich - `classify-samples` and `regress-samples` are now :qiime2: Pipelines! Effect on users: multiple different outputs are now produced, including trained classifiers for re-use!
- @Nicholas_Bokulich - β **API Breaking Changes** β`predict` has been split into two methods: `predict-classification` and `predict-regression`; and the `SampleEstimator` semantic type now must be either `SampleEstimator[Classifier]` or `SampleEstimator[Regressor]` formats. This makes up/downstream handling more transparent for users.
- @Nicholas_Bokulich - New visualizers `Summarize` for extracting parameter settings and RFE results from trained SampleEstimators. π
- β **API Breaking Changes** β@Nicholas_Bokulich - `maturity-index` is no longer an action in q2-sample-classifier, it is now a pipeline in the q2-longitudinal plugin! (see below for more details).
- A new pipeline, `classify-samples-from-dist`, has been added. This uses a kNN classifier to classify samples on a precomputed distance matrix, rather than from a feature table. Thanks Justin Kuczynski and Alena Kuczynski for creating this action!
- [q2-types](https://docs.qiime2.org/2018.8/plugins/available/types/)
- [@HannesHolste](https://github.com/hannesholste) and @Yoshiki - bumped `scikit-bio` to the latest version, `0.5.4.` π
- @Pauline_Trinh - Added the ability for `AlphaDiversityFormat` to contain additional columns as metadata.
- @gregcaporaso - Updated the alpha diversity format transformer to include metadata.
- @cduvallet - Added `PercentileNormalized` as a varient for `FeatureTable`. π
- [q2-phylogeny](https://docs.qiime2.org/2018.8/plugins/available/phylogeny/)
- @SoilRotifer - Added new tree-building methods based on [IQ-TREE](http://www.iqtree.org/)! π
- @SoilRotifer - Added access to SSE3 / AVX2 versions of RAxML via `--p-raxml-version`. These CPU-optimized versions of RAxML will reduce run time. β©
- @turanoo - Added a new [pipeline](https://github.com/qiime2/q2-phylogeny/pull/49) to build phylogenetic trees using mafft and fasttree. π² π¦
- [q2-alignment](https://docs.qiime2.org/2018.8/plugins/available/alignment/)
- @turanoo - Updated `q2-alignment mafft ` [unit tests](https://github.com/qiime2/q2-alignment/issues/49) to remove issue caused by a newer MAFFT version. π
- @turanoo - Added the `parttree` parameter to `mafft` allowing alignments of greater than 1 million sequences in the QIIME 2 plugin.
- @turanoo - Fixed a regression in the `n-threads` parameter that prevented MAFFT from using all cores.
- [q2-gneiss](https://docs.qiime2.org/2018.8/plugins/available/gneiss/)
- β **API Breaking Changes** β
- `ilr-transform` has been replaced by `ilr-hierarchical` and `ilr-phylogenetic`. Thanks [@qiyunzhu](https://github.com/qiyunzhu)!
- This plugin no longer makes use of the `FeatureTable[Composition]` type, instead pseudocounts have been added as parameters to the following methods:
- `ilr-hierarchical`
- `ilr-phylogenetic`
- `balance-taxonomy`
- `dendrogram-heatmap`
- `correlation-clusterin`
- Additionally the pseudocount behavior now defaults to _replacement_ of `0` values with `0.5`. This can be adjusted with the `pseudocount` parameter. This value is not added to non-zero observations (like in `composition add-pseudocount`).
- [q2-longitudinal](https://docs.qiime2.org/2018.8/plugins/available/longitudinal/)
- Added a new pipeline, `feature-volatility` for identifying features that are predictive of sampling time (or other continuous metadata) β see the [tutorial](https://docs.qiime2.org/2018.8/tutorials/longitudinal/) for details! Thank you @thermokarst for building the `plot-feature-volatility` visualizer, the crowning gem of this pipeline. π
- @Nicholas_Bokulich - `individual_id_column` is now an optional parameter for the visualizer `volatility`! This means that `volatility` can be used for visualizing changes in metrics across any type of continuous data, not only longitudinal experiments where the same subjects were sampled repeatedly! π
- @Nicholas_Bokulich - updated `state_column` parameter descriptions for several methods to specify how that metadata column is handled by paired-sample vs. longitudinal methods.
- β **API Breaking Changes** β@Nicholas_Bokulich - `maturity-index`, formerly in q2-sample-classifier, is now a pipeline in the q2-longitudinal plugin! This is because it is almost exclusively a longitudinal method (and so it was designed to be). Additionally, it is now a **pipeline** and the outputs and tests performed internally have been modified (and improved) extensively.
- [Virtual Machines](https://docs.qiime2.org/2018.8/install/virtual/docker/)
- @johnbradley - More versatile configuration of Docker image! π
- [q2-vsearch](https://docs.qiime2.org/2018.8/plugins/available/vsearch/)
- @colinbrislawn - Added `--derep_prefix` parameter to `vsearch dereplicate-sequences` plugin in order to support [prefix dereplication](https://www.drive5.com/usearch/manual6/dereplication.html). π
- [q2-composition](https://docs.qiime2.org/2018.8/plugins/available/composition/)
- Reimplemented the volcano plot in `ancom` with [Vega](https://vega.github.io/vega/). This corrects the bokeh problem we encountered last release. Thanks @thermokarst, @turanoo, and @Nicholas_Bokulich!
- [q2-emperor](https://docs.qiime2.org/2018.8/plugins/available/emperor/) - by @Yoshiki and @Antgonza
- This plugin is now using the latest version of emperor (1.0.0beta17).
- For very large datasets responsive plots can now be rendered live in the browser. Checkout [this example](https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fcdn.rawgit.com%2Fknightlab-analyses%2Fstriped-unifrac%2F16cb89a0%2Fqzs%2Fpcoa.qzv) with ~114K samples (courtesy of @wasade).
- Fixes a glitch that would happen after re-centering the camera and panning around the scene.
- Adds a new visualizer (`qiime emperor biplot`) to plot the results from `qiime diversity pcoa-biplot`. This method optionally expects feature metadata, this will allow you to modify visual aspects of the Biplot arrows. For an example see this animated GIF: 
Happy QIIME-ing! π
---
### Author:  [@q2d2](https://forum.qiime2.org/u/q2d2)
#### Post date: [September 6, 2018, 8:54pm UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/3 "2018-09-06T20:54:15Z")
The QIIME 2 Virtual Machines are now available! We have QIIME 2 2018.8 available on AWS, Docker, and VirtualBox, please [see the docs](https://docs.qiime2.org/2018.8/install/virtual/) for more information. Thanks! π
---
### Author:  [@q2d2](https://forum.qiime2.org/u/q2d2)
#### Post date: [September 14, 2018, 1:10pm UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/4 "2018-09-14T13:10:34Z")
It appears that the QIIME 2 Studio build in the VirtualBox image is currently broken. We are working towards pushing up a new build, but it might take a week or two. If you would like to use the Studio, please check out [QIIME 2 Studio (q2studio) β QIIME 2 2018.8.0 documentation](https://docs.qiime2.org/2018.8/interfaces/q2studio/) for installation directions. Thanks! :qiime2:
---
### Author:  [@q2d2](https://forum.qiime2.org/u/q2d2)
#### Post date: [September 20, 2018, 11:33pm UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/6 "2018-09-20T23:33:51Z")
A new build (`1537275675`) has been pushed up - please update if you want QIIME 2 Studio, otherwise the build is unchanged. Thanks!
---
### Author:  [@bsen2018](https://forum.qiime2.org/u/bsen2018)
#### Post date: [November 5, 2018, 3:18am UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/8 "2018-11-05T03:18:50Z")
Hi! @q2d2,
Just curious to know the expected data of release of QIIME2 2018.10, because I am waiting to install it in a new laptop. Thanks!
BS
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 5, 2018, 3:49am UTC](https://forum.qiime2.org/t/qiime-2-2018-8-release-is-now-live/5860/10 "2018-11-05T03:49:31Z")
The next release is 2018.11:
> [@\[Preview\] QIIME 2 2018.11 development changelog](https://forum.qiime2.org/t/preview-qiime-2-2018-11-development-changelog/6310):
>
> QIIME 2 2018.11 has been released! [Please see the official changelog for more details.](https://forum.qiime2.org/t/qiime-2-2018-11-release-is-now-live/6879)arrow_forward Original content of post
Scheduled to come out this week π€