This page tells you how to install HybSuite step by step.
HybSuite is a shell-based tool, invoking some python and R scripts, which is only available for Linux/Unix/WSL/macOS users.
Installing HybSuite via conda is strongly recommended, meanwhile manual installation is also available.
1. Install HybSuite via conda
(1) Prerequisites
- Conda installation is required. If you don’t already have conda installed, see here for instructions on installing Anaconda or Miniconda.
(2) Step-by-step installation
To avoid dependency conflicts, creating a new conda environment for HybSuite is more recommended:
conda create -n hybsuite
And then, you can activate your newly-created conda environment and install hybsuite using the command below directly (from the specified channel):
conda activate hybsuite
conda install yuxuanliu::hybsuite
Before installing hybsuite, you can edit your ~/.condarc file as this to avoid installation issues about conda channels:
channels:
- conda-forge
- bioconda
- yuxuanliu
- defaults
Our official bioconda channel package is currently under review. Until approved, using the command showed above is also useful.
(3) Verification
After installation, you can check the help menu of HybSuite to confirm successful installation by running:
hybsuite -h
2. Install HybSuite manually
(1) Prerequisites
- Conda installation is required. If you don’t already have conda installed, see here for instructions on installing Anaconda or Miniconda.
(2) Package installtion
Directly clone the github repository:
git clone https://github.com/Yuxuanliu-HZAU/HybSuite.git
(3) Verification
After installation, you can check the help menu of HybSuite to confirm successful installation by running:
bash <absolute or relative path to HybSuite.sh> -h
(4) Dependencies installtion
Method 1: Run Install_all_dependencies.sh to install all dependencies in one go (more recommended)
The most convenient way to install all dependencies for HybSuite is directly running our script: HybSuite-master/Install_all_dependencies.sh to install all desired dependencies.
Before running this script, activate your target conda environment.
conda activate <conda_environment_name>
bash HybSuite-master/Install_all_dependencies.sh
Method 2: Install dependencies manually
If you fail to install some dependencies when running Install_all_dependencies.sh, then it is more advisable to install dependencies manually. Just follow the following steps:
conda create -n <conda_environment_name>
conda activate <conda_environment_name>
conda install conda-forge::mamba -y
mamba install python=3.9.15 -y
mamba install bioconda::hybpiper -y
mamba install bioconda::paragone -y
mamba install bioconda::amas -y
mamba install bioconda::sra-tools -y
mamba install conda-forge::pigz -y
conda install conda-forge::plotly -y
mamba install bioconda::newick_utils -y
mamba install bioconda::mafft -y
mamba install bioconda::trimal -y
mamba install bioconda::iqtree -y
mamba install bioconda::raxml -y
mamba install bioconda::raxml-ng -y
mamba install bioconda::aster -y
mamba install r
pip install ete3
pip install PyQt5
pip install phylopypruner
pip install phykit
R
install.packages("phytools")
install.packages("ape")