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Troubleshooting Guide

Installation

Long Story Short

# 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 flexible

# Install DAJIN2 to a virtual environment
conda create -n env-dajin2 python=3.10 -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 is highly recommended for managing dependencies
  • If using pip, access to administrative privileges or the ability to install packages globally

Dependencies

DAJIN2 depends on the pysam package, which in turn requires htslib. These dependencies are critical for the functionality of DAJIN2 but can pose installation challenges:

  • htslib requires zlib.h, which may not be available on all systems by default.
  • As of the latest update, htslib v1.18, there is no support for Windows via Bioconda.

Recommended Installation Method

Using Conda/Mamba

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

  1. Install the latest Conda if you have not already. You can download Conda from here.

  2. Setup the Bioconda channel:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority flexible

Note

Bioconda recommends using conda config --set channel_priority strict, but as the installation of openpyxl fails, please use conda config --set channel_priority flexible.

  1. Create a new virtual environment (optional but recommended):
conda create -n env-dajin2
conda activate env-dajin2
  1. Install DAJIN2 in the virtual environment:
conda install -c bioconda DAJIN2

Using pip

If you prefer or are required to use pip, please ensure that zlib.h and other dependencies are properly installed on your system. This method might require administrative privileges:

pip install DAJIN2

Note

Pip installation might encounter issues due to the dependencies mentioned above, especially on systems without zlib.h or on Windows. sudo apt install gcc zlib1g zlib1g-dev (Ubuntu)
brew install gcc zlib (macOS)

Report other troubles

Please use GitHub Issues for all reporting purposes.