beast2.qmd

---
title: "Install, setup, and run BEAST2 on Atlas HPC"
description: "Using BEAST, TreeAnnotator, and other beastily things"
date: "2024-08-23"
about:
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format: 
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     toc-depth: 2
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---

## Initiate Conda

### **1. Open a Shell**
Open a shell on Atlas and navigate to your project directory.


### **2. Load the Miniconda3 Module**
```bash
module load miniconda3
```

### **3. Initialize Conda**
Initialize Conda to work with your shell:

```bash
conda init
```
### **4. Close and Reopen Your Shell**

You may need to restart your shell session.  Close your terminal window and open a new one.

## Create Conda Environment
### **5. Create a New Conda Environment for BEAST2**

Creating an environment helps manage dependencies.  In the code below, replace `beast2_env` with any name of your choosing.  

```bash
conda create -n beast2_env
```

- When prompted, type `Y` to proceed with the environment creation.

### **6. Activate the Conda Environment**

```bash
conda activate beast2_env
```

You should see the environment name prefixed in your shell prompt (before your username).  

### **7. Configure Conda Channels**

Add the necessary channels to install BEAST2 and its dependencies. 

```bash
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels defaults
```

```bash
conda config --show channels
```

You should see:

```
channels:
  - conda-forge
  - bioconda
  - defaults
```

---
## Install BEAST2 

### **8. Install BEAST2 via Conda**

Now, install BEAST2 using Conda:

```bash
conda install -c bioconda beast2
```

- Type `Y` when prompted to proceed with the installation.
- Conda will resolve dependencies and install BEAST2 along with the appropriate Java version.

### **9. Verify the Installation**

```bash
beast -help
```

You should see usage information for BEAST2.

### **10. Ensure `treeannotator` Is Available**

```bash
which treeannotator
```

If the path to `treeannotator` is displayed, it means the command is available.

## Test Run  

### **11. Run `treeannotator`**

Now you can run `treeannotator` using the alias or the command.

##### **Example Command:**

Assuming that the `fmd-viet-treelog.trees` file are

```bash
treeannotator -burnin 10 -heights median fmd-viet-treelog.trees atlas_test.tre
```

*Ensure that you are in the directory containing your input file `fmd-viet-treelog.trees` or provide the full path to the file.*



## End Session

### **12. Deactivate the Conda Environment When Done**

After you're finished, you can deactivate the environment:

```bash
conda deactivate
```