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Update README.md to remove outdated references to the Intel conda environment. #5753

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9 changes: 3 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -81,16 +81,13 @@ releases of the toolkit.
* First, make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient).
* 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, or the command ```conda env create -f gatkcondaenv.intel.yml``` to create
the ```gatk-intl``` environment.
create the ```gatk``` environment.
* If running from a cloned repository, run ```./gradlew localDevCondaEnv```. This generates the Python
package archive and conda yml dependency file(s) in the build directory, and also creates (or updates)
the local ```gatk``` conda environment. (To create the ```gatk-intel``` conda environment once the files
have been generated, run the command ```conda env create -f gatkcondaenv.intel.yml```).
the local ```gatk``` conda environment.
* To "activate" the conda environment (the conda environment must be activated within the same shell from which
GATK is run):
* Execute the shell command ```source activate gatk``` to activate the ```gatk``` environment, or
```source activate gatk-intel``` to activate the ```gatk-intel``` environment.
* Execute the shell command ```source activate gatk``` to activate the ```gatk``` environment.
* See the [Conda](https://conda.io/docs/user-guide/tasks/manage-environments.html) documentation for
additional information about using and managing Conda environments.

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