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MAINT: removes local download for tiny env file
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lizgehret authored and gregcaporaso committed Jul 18, 2024
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42 changes: 11 additions & 31 deletions book/plugins/how-to-guides/set-up-development-environment.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,43 +16,36 @@ If you expect that you might need help setting up your development environment,
{{ miniconda_url }} provides the ``conda`` environment and package manager, and is currently the only supported way to install QIIME 2.
Follow the instructions for downloading and installing Miniconda.

After installing Miniconda and opening a new terminal, make sure you're running the latest version of ``conda`` (and get a copy of ``wget``, while you're at it):
After installing Miniconda and opening a new terminal, make sure you're running the latest version of ``conda``:

```bash
conda update conda
conda install wget
```

## Install the latest development version of the QIIME 2 "Tiny Distribution"

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" or "Shotgun" distributions, 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 QIIME 2 distributions, such as the "Amplicon" or "Metagenome" distributions, in which case see [](other-distros).
```

`````{tab-set}
````{tab-item} macOS
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda env create -n q2dev-tiny --file qiime2-tiny-macos-latest-conda.yml
rm qiime2-tiny-macos-latest-conda.yml
conda env create -n q2dev-tiny --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
```
````
````{tab-item} Linux
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
conda env create -n q2dev-tiny --file qiime2-tiny-ubuntu-latest-conda.yml
rm qiime2-tiny-ubuntu-latest-conda.yml
conda env create -n q2dev-tiny --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
```
````
````{tab-item} macOS (Apple Silicon)
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-tiny --file qiime2-tiny-macos-latest-conda.yml
rm qiime2-tiny-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-tiny --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda config --env --set subdir osx-64
```
````
Expand Down Expand Up @@ -134,25 +127,19 @@ If you install a distribution other than the "Tiny Distribution", be sure that t
`````{tab-set}
````{tab-item} macOS
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda env create -n q2dev-amplicon --file qiime2-amplicon-macos-latest-conda.yml
rm qiime2-amplicon-macos-latest-conda.yml
conda env create -n q2dev-amplicon --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
```
````
````{tab-item} Linux
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
conda env create -n q2dev-amplicon --file qiime2-amplicon-ubuntu-latest-conda.yml
rm qiime2-amplicon-ubuntu-latest-conda.yml
conda env create -n q2dev-amplicon --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
```
````
````{tab-item} macOS (Apple Silicon)
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-amplicon --file qiime2-amplicon-macos-latest-conda.yml
rm qiime2-amplicon-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-amplicon --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda config --env --set subdir osx-64
```
````
Expand All @@ -163,27 +150,20 @@ conda config --env --set subdir osx-64
`````{tab-set}
````{tab-item} macOS
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
conda env create -n q2dev-metagenome --file qiime2-metagenome-macos-latest-conda.yml
rm qiime2-metagenome-macos-latest-conda.yml
conda env create -n q2dev-metagenome --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
```
````
````{tab-item} Linux
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-ubuntu-latest-conda.yml
conda env create -n q2dev-metagenome --file qiime2-metagenome-ubuntu-latest-conda.yml
rm qiime2-metagenome-ubuntu-latest-conda.yml
conda env create -n q2dev-metagenome --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-ubuntu-latest-conda.yml
```
````
````{tab-item} macOS (Apple Silicon)
```bash
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-metagenome --file qiime2-metagenome-macos-latest-conda.yml
rm qiime2-metagenome-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-metagenome --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
conda config --env --set subdir osx-64
```
````
`````

3 changes: 2 additions & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
@@ -1 +1,2 @@
jupyter-book
jupyter-book
q2doc@git+https://github.com/qiime2/sphinx-ext-qiime2.git@master

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