Installation

This tool requires a number of third-party software packages. Before installation, please make sure you are working within a Linux environment and that git, conda or mamba are already installed.

1. Dependency installation

  • python = 3.11

  • pysam = 0.22.0

  • biopython = 1.81

  • samtools = 1.18

  • minimap2 = 2.27

  • bwa = 0.7.17

  • Flye = 2.9.4

  • pilon = 1.2.4

  • NextPolish = 1.4.1

  • GenomeSyn = 1.2.7

1.1 NextPolish (recommended: install from source)

$ git clone https://github.com/shilong-liu/NextPolish.git
$ cd NextPolish
$ make

Add NextPolish to your PATH (recommended):

$ echo "export PATH=\$PATH:/path/to/NextPolish" >> ~/.bashrc
$ source ~/.bashrc

1.2 Other dependencies: They can be installed via conda, or downloaded and installed from their GitHub repositories, or installed automatically by running the install.sh script provided with TeloComp.

2. Linux Installation

To use the software, you need to follow the following steps to install it.

2.1 Obtain software package from GitHub: Open the software’s GitHub repository, e.g., https://github.com/lxie-0709/TeloComp. Click the “Code” button and select “Download ZIP” to get the package, or copy the repository URL for git clone. To clone via command line:

$ git clone git@github.com:lxie-0709/TeloComp.git
$ cd TeloComp

2.2 Install dependencies and configure the software. Please install the required dependencies under the Dependencies/ directory and configure the executable programs in the ``bin/``directory, respectively. The Dependencies folder is intended for third-party dependency packages, whereas the bin directory contains or links to the actual tools to be executed.

(1)Installing dependencies

$ sh install.sh

(2)Configuring TeloComp

$ sh setup.sh

3.Install GenomeSyn

Download GenomeSyn and place the uncompressed GenomeSyn-1.2.7 directory under your root path (/yourPATH/). Set the execution permission and add the binaries to your system PATH:

$ chmod +x GenomeSyn-1.2.7
$ echo "export PATH=\$PATH:/yourPATH/GenomeSyn-1.2.7/bin" >> ~/.bashrc
$ source ~/.bashrc

4. Verify Installation

Check that all required tools are available:

# Activation environment
$ source ~/.bashrc

$ telocomp_Filter_1 -h

$ telocomp_Filter_2 -h

$ telocomp_Assembly -h

$ telocomp_maxmin -h

$ telocomp_Complement -h

$ telocomp_Collinearity -h

If the help message of each command is printed, the installation has been completed successfully.

Tip

Please open an issue on GitHub for feature requests or bug reports.