# QIIME 2 2025.4 breaking changes & environment files
**URL:** https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475
**Category:** Announcements
**Tags:** environment-files
**Created:** [February 7, 2025, 12:26am UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475 "2025-02-07T00:26:49Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [February 7, 2025, 12:26am UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/1 "2025-02-07T00:26:49Z")
**Hello QIIME 2 Developer community! 🤓👋🏼**
Below is the list of guaranteed interface changes, plugin API changes, and environment file updates for the 2025.4 QIIME 2 release. You can use the linked environment files for each distribution to ensure compatibility with any plugin you're developing against the relevant distribution it should be tested/used within. Note that these 'seed' environment files won't change between now and the 2025.4 release, but the full environment files that conda will resolve at any given installation will change. This shouldn't impact your development process, as all of the core dependencies in these 'seed' files will remain the same.
* * *
**Interface Changes 📺**
- [q2-dada2](https://github.com/qiime2/q2-dada2)
- The `pooled` option to the `--p-chimera-method` parameter was removed as it should only be used in tandem with other parameter options that are not available in QIIME2.
* * *
**Plugin API Changes 🔌**
* * *
**Environment File Changes 🗃**
**NOTE** : The metagenome distribution has been renamed to moshpit!
- [tiny](https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.4/tiny/passed/seed-environment-conda.yml)
- biom-format has been bumped to 2.1.16
- rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
- scikit-bio has been bumped to 0.6.2
- [amplicon](https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.4/amplicon/passed/seed-environment-conda.yml)
- rpy2 has been added as a new external dependency to support the new ANCOM-BC2 wrapper within [q2-composition](https://github.com/qiime2/q2-composition)
- biom-format has been bumped to 2.1.16
- fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
- r-vegan has been bumped to 2.6\_8
- rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
- scikit-bio has been bumped to 0.6.2
- vsearch 2.22.1 has been added as a new dependency to match the existing pins in moshpit and pathogenome
- [moshpit](https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.4/moshpit/passed/seed-environment-conda.yml)
- [q2-alignment](https://github.com/qiime2/q2-alignment) has been added as a new QIIME 2 dependency, as [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt) now depends on it.
- q2-moshpit has been renamed to [q2-annotate](https://github.com/bokulich-lab/q2-annotate)
-
- q2-annotate's inputs/outputs have been renamed to ensure consistency between different actions. Methods affected include: classify\_kraken2, collate\_kraken2\_reports, collate\_kraken2\_outputs, estimate\_bracken, kraken2\_to\_mag\_features, fetch\_eggnog\_db, fetch\_diamond\_db, search\_orthologs\_diamond, search\_orthologs\_hmmer, map\_eggnog, collate\_busco\_result, evaluate\_busco, predict\_genes\_prodigal, fetch\_busco\_db, and estimate\_abundance 🔄
- biom-format has been bumped to 2.1.16
- fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
- mafft has been pinned at 7.526 due to second order dependencies
- rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
- scikit-bio has been bumped to 0.6.2
- spades has been bumped to 4.0.0
- [pathogenome](https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.4/pathogenome/passed/seed-environment-conda.yml)
- biom-format has been bumped to 2.1.16
- mafft has been pinned at 7.526 due to second order dependencies
- rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
- scikit-bio has been bumped to 0.6.2
- spades has been bumped to 4.0.0
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [February 7, 2025, 3:03pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/2 "2025-02-07T15:03:26Z")
2 off-topic replies have been split into a new topic: [the pooled option to the --p-chimera-method parameter in q2-dada2](https://forum.qiime2.org/t/the-pooled-option-to-the-p-chimera-method-parameter-in-q2-dada2/32480)
Please keep replies on-topic in the future.
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### Author:  [@yawei](https://forum.qiime2.org/u/yawei)
#### Post date: [April 1, 2025, 8:05am UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/4 "2025-04-01T08:05:43Z")
Hi，does anyone can tell me， when will the 2025.4 version be released？
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [April 1, 2025, 3:13pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/5 "2025-04-01T15:13:40Z")
Hi @yawei,
Our planned release date is April 16th (though we reserve the right to bump this date barring any unexpected issues that may come up). We will post a formal announcement when the release is live.
Cheers 🦎
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### Author:  [@yawei](https://forum.qiime2.org/u/yawei)
#### Post date: [April 2, 2025, 12:53am UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/6 "2025-04-02T00:53:54Z")
Hi, @ [lizgehret](https://forum.qiime2.org/u/lizgehret), thank you so mush for your reply！Looking forward to the release of the new version and hoping that I can install it normally.
Cheers,
Yawei
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### Author:  [@yawei](https://forum.qiime2.org/u/yawei)
#### Post date: [April 18, 2025, 7:09pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/7 "2025-04-18T19:09:23Z")
Hello，@ [lizgehret](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/5)， is there any new update about the release time of the 2025.4 distribution?
Thanks in advance!
Cheers,
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### Author:  [@lizgehret](https://forum.qiime2.org/u/lizgehret)
#### Post date: [April 18, 2025, 9:31pm UTC](https://forum.qiime2.org/t/qiime-2-2025-4-breaking-changes-environment-files/32475/8 "2025-04-18T21:31:24Z")
Hi @yawei,
We had to bump the release date to tie up some loose ends. We currently anticipate it being released next week. We will post a formal announcement when the release is live.
Cheers 🦎