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Code review update.
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cmnbroad committed May 21, 2018
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Expand Up @@ -72,13 +72,13 @@ releases of the toolkit.
* Pre-packaged Docker images with all needed dependencies installed can be found on
[our dockerhub repository](https://hub.docker.com/r/broadinstitute/gatk/). This requires a recent version of the
docker client, which can be found on the [docker website](https://www.docker.com/get-docker).
* Python Dependencies<a name="python"></a>
* GATK uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the
environment and dependencies required by GATK tools that use Python There are two different conda environments
* Python Dependencies:<a name="python"></a>
* GATK4 uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the
environment and dependencies required by GATK tools that use Python. There are two different conda environments
that can be used:
* The "gatk" environment, which has no special hardware requirements.
* The "gatk" environment, which has no special hardware requirements. The GATK Docker image comes with the
"gatk" environment pre-configured.
* The "gatk-intel" environment, which requires and uses Intel hardware acceleration to increase performance.
* The GATK Docker image comes with the "gatk" environment pre-configured.
* In order to establish the conda environment required to run these tools when not using the Docker image, do
the following:
* Make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient).
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