How to install biometric software in Linux system? A complete nanny guide

Linux biometric software installation guide

There are usually multiple ways to install bioinformatics analysis software under Linux systems, including installation using package management tools (such as conda) and compilation and installation through source code. This note briefly shares the methods and techniques for installing bioinformatics analysis software under Linux. I hope it will be helpful to you. It is recommended to forward it and collect it!

This article will take vcftools as an example to demonstrate the steps and methods of software installation using conda and compilation and installation.

Use conda to install (recommended)

conda is an open source software package management system that can be used to install and manage bioinformatics analysis software. Here are the steps to install vcftools using conda:

First, make sure you have conda installed

https://docs.conda.io/projects/miniconda/en/latest/<br>

Open a terminal and create a new conda environment

The purpose of creating an environment is to isolate dependencies between different software packages and avoid conflicts.

conda create -n myenv<br>

Where myenv is the name of the environment, which can be modified according to your own needs.

The environment here is equivalent to different small rooms, each performing its own duties without affecting each other.

For example, build a new kitchen, install a gas stove in it, and then install a range hood and use it normally.

Suddenly one day, you want to install a TV on a whim. Experience tells you that you should build a new living room, which would be better for installing the TV. Although it can be watched in the kitchen, who can watch TV while chopping vegetables?

After a while, I wanted to go to the toilet, and I needed to install a toilet urgently. In my desperation, I forgot to create a new environment and installed the toilet directly in the kitchen. That would be interesting, but there was a conflict at startup and I couldn’t go to the toilet while cooking.

In the above short story, the kitchen, living room and toilet are like different conda environments. The toilet, gas stove, range hood and TV are like software tools. Sometimes multiple software must be installed in the same environment to use (such as range hood The machine and gas stove are both in the kitchen), but sometimes different software must be installed in different environments (for example, the toilet and gas stove cannot be placed together).

(The end of the short story, let’s get back to the main story)

Activate the newly created environment.
```
conda activate myenv 
```
Use conda to install vcftools.
```
conda install -c bioconda vcftools 
```
This command will download and install vcftools and its dependencies from the bioconda channel. There are different warehouse channels that store different software. You can choose according to the actual situation.
After the installation is complete, you can use the following command to verify whether vcftools was successfully installed. If the installation is successful, the version information of vcftools will be displayed.
```
vcftools --version 
```

What is the difference between conda and mamba?

Compile and install

If you cannot use conda to install vcftools, or you need to customize the compilation options, you can choose to compile and install from source code. The following are the steps to install vcftools using the compile installation method:

First, install the necessary compilation tools and dependencies. In Ubuntu systems, you can use the following commands to install the required packages.
```
sudo apt-get update sudo apt-get install build-essential zlib1g-dev 
```
Other Linux distributions can be installed according to their own package managers.
Download the source code of vcftools. The source code can be obtained from the official website of vcftools or the GitHub repository.
```
wget https://github.com/vcftools/vcftools/archive/refs/tags/v0.1.16.tar.gz tar -zxvf v0.1.16.tar.gz cd vcftools-0.1.16 
```
Compile and install vcftools.
```
make sudo make install 
```
This will compile the source code and install the executable into the system path.
After the installation is complete, you can use the following command to verify whether vcftools was successfully installed.
```
vcftools --version 
```

Summary

This article introduces two common ways to install bioinformatics analysis software under Linux systems: installation using conda and compilation and installation through source code. Taking vcftools as an example, the specific installation steps and methods are demonstrated. Depending on the actual situation, choosing an appropriate installation method can make bioinformatics analysis more convenient.

Tips for tips

When installing software, consider installing it through conda first. You can first search for any ready-made yml configuration files and copy other people’s homework to improve efficiency.
If the conda installation prompts that it is not found, it is most likely that the warehouse is incorrect or there is a spelling error.
Don’t install all the software at once. Generally, install what you need based on your own analysis.
If you need a specific version when installing software, be sure to pay attention to whether it conflicts with the existing version, otherwise the old software will suddenly become unusable after installing the new software.
Try to use the official help document method for installation. If there are errors, it is convenient to ask questions.
If you are installing Java-type software, you must also consider the JDK environment.
If the server cannot be connected to the Internet, it is recommended to use your own computer to install the virtual machine, and directly package and transplant it after the installation is complete.
If you have enough energy to learn, you can learn about container technologies such as docker and singularity, which may open the door to a new world.

The above is an introduction to the steps and methods of installing bioinformatics analysis software under Linux systems. I hope it will be helpful to you!

This article is published by mdnice multi-platform