From cefed0ff4d04282b9915486be07de85b2b77b657 Mon Sep 17 00:00:00 2001
From: akikuno <akikuno@users.noreply.github.com>
Date: Mon, 25 Dec 2023 11:09:22 +0900
Subject: [PATCH] Added a short form of installation guide to
 TROUBLESHOOTING.md

---
 docs/TROUBLESHOOTING.md | 40 ++++++++++++++++++++++++++++++++++------
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index eb232ec6..fff79ac1 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -2,13 +2,31 @@
 
 ## 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
@@ -24,15 +42,25 @@ Before installing `DAJIN2`, please ensure that your system meets the following r
 
 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
 ```