Installation Conda - MeryemAk/dRNASeq GitHub Wiki

This guide provides instructions for setting up the necessary environment and tools for your project on a Linux system. It covers both automated and manual installation methods.

Clone GitHub repository
Automated Installation
Manual Installation
- Miniconda Installation
- Conda Environment Setup
Conda Environment Creation (Detailed)

1. Clone GitHub repository

Before proceeding with either automated or manual installation, you need to clone the project's GitHub repository to your local machine. This will ensure you have all the necessary files, including the installation scripts and environment configuration.

git clone https://github.com/MeryemAk/dRNASeq
cd dRNASeq

2. Automated Installation

The 1.linuxsetup.sh script automates the installation of Miniconda and the setup of the Conda environment.

Prerequisites: Before running the script, it's recommended to update your system:
```
sudo dnf update
```
Running the script:
1. Save the 1.linuxsetup.sh script to a directory on your computer.
2. Navigate to the directory containing the script in your terminal.
3. Execute the script:
```
bash 1.linuxsetup.sh
```
Post-installation:
- Restart your terminal session to apply the changes.
- Activate the environment:
```
conda activate dRNAseq
```
- Deactivate the environment:
```
conda deactivate
```

3. Manual Installation

This section details the manual steps to install Miniconda and set up the Conda environment.

2.1 Miniconda Installation

These steps are based on manual_setup_linux.txt.

Create a directory for Miniconda:
```
mkdir -p ~/miniconda3
```

Download the Miniconda installer:

wget [https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh](https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh) -O ~/miniconda3/miniconda.sh

Run the installer:

bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

Remove the installer script:
```
rm ~/miniconda3/miniconda.sh
```
Refresh the terminal:
```
source ~/miniconda3/bin/activate
```
Initialize Conda:
```
conda init --all
```

Verify Installation: To check if Miniconda is installed, run:
```
conda list
```
If Miniconda is not installed, you'll see the message bash: conda: command not found.
More Information: https://www.anaconda.com/docs/getting-started/miniconda/install#linux

2.2 Conda Environment Setup

These steps are also from manual_setup_linux.txt.

Clone the repository:

git clone [https://github.com/MeryemAk/dRNASeq](https://github.com/MeryemAk/dRNASeq)
cd dRNASeq

Check for the environment file:
```
ls
```
Create the Conda environment:
```
conda env create -f environment.yml
```
Activate the environment:
```
conda activate dRNAseq
```

4. Conda Environment Creation (Detailed)

The conda_env_creation.md file provides a detailed breakdown of creating the Conda environment and installing the necessary tools.

Create and activate the environment:

conda create -n dRNAseq
conda activate dRNAseq
conda config --show channels   # Verify channels: bioconda, conda-forge, defaults

Install tools:

conda install -c bioconda nanopack
conda install -c nanoporetech -c conda-forge -c bioconda "nanoporetech::pychopper"
conda install bioconda::minimap2
conda install -c bioconda samtools
conda install -c bioconda subread

Resolve samtools error (if needed):

conda install python=3.10
conda install -c bioconda samtools

Verify installation:

conda list | grep toolname  # Replace 'toolname'

This comprehensive guide should help users set up your project effectively!