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Added a short form of installation guide to TROUBLESHOOTING.md
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akikuno committed Dec 25, 2023
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## Installation

### Long Story Short

```bash
# Update conda
conda update -n base conda -y

# Setup of Bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# Install DAJIN2 to a virtual environment
conda create -n env-dajin2 -y
conda activate env-dajin2
conda install -c bioconda DAJIN2 -y
```

### Prerequisites

Before installing `DAJIN2`, please ensure that your system meets the following requirements:

- Python >=3.7
- Unix-like environment (Linux, macOS, WSL, etc.)
- [conda](https://docs.conda.io/en/latest/) or [mamba](https://mamba.readthedocs.io/en/latest/) is highly recommended for managing dependencies
- [Conda](https://docs.conda.io/en/latest/) is highly recommended for managing dependencies
- If using pip, access to administrative privileges or the ability to install packages globally

### Dependencies
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We strongly recommend using Conda or Mamba for installation, as they efficiently manage the complex dependencies of `pysam` and `htslib`:

1. Install Conda or Mamba if you haven't already. You can download Conda from [here](https://docs.conda.io/en/latest/miniconda.html).
1. Install the latest Conda if you have not already. You can download Conda from [here](https://docs.conda.io/en/latest/miniconda.html).

2. Setup the [Bioconda](https://bioconda.github.io/) channel:

```bash
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
```

3. Create a new virtual environment (optional but recommended):

2. Create a new environment (optional but recommended):
```bash
conda create -n DAJIN2-env
conda activate DAJIN2-env
conda create -n env-dajin2
conda activate env-dajin2
```

3. Install `DAJIN2`:
4. Install `DAJIN2` in the virtual environment:
```bash
conda install -c bioconda DAJIN2
```
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