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Add more detailed conda setup instructions to the GATK README (#9001)
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Our README was missing some important details on how to properly setup the GATK conda environment locally.
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droazen authored Oct 16, 2024
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Expand Up @@ -79,15 +79,31 @@ releases of the toolkit.
docker client, which can be found on the [docker website](https://www.docker.com/get-docker).
* Python Dependencies:<a name="python"></a>
* GATK4 uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the
Python environment and dependencies required by GATK tools that have a Python dependency. This environment also
includes the R dependencies used for plotting in some of the tools. The ```gatk``` environment
requires hardware with AVX support for tools that depend on TensorFlow (e.g. CNNScoreVariant). The GATK Docker image
comes with the ```gatk``` environment pre-configured.
* At this time, the only supported platforms are 64-bit Linux distributions. The required Conda environment is not
currently supported on OS X/macOS.
Python environment and dependencies required by Python-based GATK tools. This environment also
includes the R dependencies used for plotting in some of the tools. The GATK Docker image
comes with the ```gatk``` conda environment pre-configured and activated.
* To establish the environment when not using the Docker image, a conda environment must first be "created", and
then "activated":
* First, make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient).
* First, make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed. We recommend installing
```Miniconda3-py310_23.10.0-1``` from [the miniconda download page](https://repo.anaconda.com/miniconda/), selecting the Linux or
MacOS version of the installer as appropriate.
* This is the same version of ```miniconda``` used by the official GATK docker image.
* If you use a different version, you may run into issues.
* If you have an ARM-based Mac, you must select the `MacOSX-x86_64` installer, not the `MacOSX-arm64` installer,
and rely on Mac OS's built-in x86 emulation.
* Set up miniconda:
* Install miniconda to a location on your PATH such as ```/opt/miniconda```, and then restart your shell:
```
bash Miniconda3-py310_23.10.0-1-[YOUR_OS].sh -p /opt/miniconda -b
```
* Disable conda auto-updates, which can cause compatibility issues with GATK:
```
conda config --set auto_update_conda false
```
* Enable the (much) faster ```libmamba``` solver to greatly speed up creation of the conda environment:
```
conda config --set solver libmamba
```
* To "create" the conda environment:
* If running from a zip or tar distribution, run the command ```conda env create -f gatkcondaenv.yml``` to
create the ```gatk``` environment.
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