Add more detailed conda setup instructions to the GATK README #9001
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@lbergelson / @KevinCLydon , please review for accuracy / completeness of the revised conda setup instructions |
README.md
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| @@ -81,13 +81,29 @@ releases of the toolkit. | |||
| * 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 | |||
| requires hardware with AVX support for tools that depend on TensorFlow. The GATK Docker image | |||
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Are there other tools in GATK that use Tensorflow?
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Yeah, you're right, the mention of Tensorflow will be obsolete once the CNN tools are removed. Pytorch, however, does apparently depend on the Intel MKL, which uses CPU-based features for acceleration:
| * 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 |
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Should we add a parenthetical note saying that you might run into issues if you try to use a different conda version?
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Yes, we definitely should!
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What is the opt folder and why do we install there? I've never understood linux folder structures...
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According to one of my AI friends:
The /opt directory in Linux is a reserved space for installing optional or add-on software packages. The name /opt stands for "optional".
The /opt directory is important for several reasons, including:
- System management
- The /opt directory helps keep the Linux system organized and modular, which makes it easier to manage and maintain.
- Security
- By separating optional software from the core system, the /opt directory reduces the risk of accidentally modifying or deleting critical system files.
- Software storage
- The /opt directory is often used to store manually compiled software, which is built from source code instead of being installed from distribution repositories.
Within the /opt directory, applications are usually stored in /opt/bin, while libraries are placed in /opt/lib
| 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: | ||
| ``` |
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At some point I ended up running conda init. I'm not clear on what that did or if it was necessary but maybe it was?
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hmm.... @KevinCLydon did you have to do that too?
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@KevinCLydon doesn't see this command in the history of commands he ran to setup his environment, so I'm going to assume it's not actually necessary.
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