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gregcaporaso merged 2 commits into from
Apr 17, 2026
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MAINT: updates env file names #170

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IMP: updates set-up-development-environment.md
gregcaporaso Apr 17, 2026
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gregcaporaso Apr 17, 2026
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54 changes: 24 additions & 30 deletions book/plugins/how-to-guides/set-up-development-environment.md
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ conda update conda
The QIIME 2 "Tiny Distribution" is a minimal set of QIIME 2 functionality for building and using plugins through the QIIME 2 command line, and is intended for use by developers who want a minimal QIIME 2 environment to work in.

```{note}
We recommend starting your development with the "Tiny Distribution", unless you specifically need plugins that are installed in other QIIME 2 distributions, such as the Amplicon Distribution or MOSHPIT (previously known as the Metagenome Distribution), in which case see [](other-distros).
We recommend starting your development with the "Tiny Distribution", unless you specifically need plugins that are installed in other rachis distributions, such as the QIIME 2 Distribution or MOSHPIT (previously known as the Metagenome Distribution), in which case see [](other-distros).
```

```{note}
Expand All @@ -44,28 +44,27 @@ Things change relatively quickly with development environments, so it doesn't hu


`````{tab-set}
````{tab-item} macOS
````{tab-item} macOS (x86_64)
```bash
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-tiny-osx-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````

````{tab-item} Linux
````{tab-item} Linux (x86_64)
```bash
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-tiny-linux-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````

````{tab-item} macOS (Apple Silicon)
````{tab-item} macOS (ARM64)
```bash
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-tiny-osx-arm64-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64
```
````
`````
Expand Down Expand Up @@ -136,29 +135,29 @@ make test
(other-distros)=
## Installing other QIIME 2 distributions

### Amplicon distribution
### qiime2 (previously known as the *Amplicon distribution*)

`````{tab-set}
````{tab-item} macOS
````{tab-item} macOS (x86_64)
```bash
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
__Q2DEV_ENV_NAME=q2dev-qiime2-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-qiime2-osx-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````

````{tab-item} Linux
````{tab-item} Linux (x86_64)
```bash
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
__Q2DEV_ENV_NAME=q2dev-qiime2-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-qiime2-linux-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````

````{tab-item} macOS (Apple Silicon)
```bash
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
__Q2DEV_ENV_NAME=q2dev-qiime2-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-qiime2-osx-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64
```
Expand All @@ -168,28 +167,23 @@ conda config --env --set subdir osx-64
### MOSHPIT (previously known as the *Metagenome distribution*)

`````{tab-set}
````{tab-item} macOS
````{tab-item} Linux (x86_64)
```bash
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-moshpit-linux-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````
`````

````{tab-item} Linux
```bash
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-ubuntu-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
```
````
### pathogenome

````{tab-item} macOS (Apple Silicon)
`````{tab-set}
````{tab-item} Linux (x86_64)
```bash
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml
__Q2DEV_ENV_NAME=pathogenome-dev-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/rachis-pathogenome-linux-64-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64
```
````
`````