How to easily manage your software using conda?

Conda is an environment and package manager which is the best and the easiest of all the competitors available in the market. The main need of the conda is to manage the software as there could be a triangle of the software where the first software will depend upon a specific version of the second software while a third software depends upon another specific version of the second software.

For these types of situations, conda provides a different environment where both versions of the software can exist without impacting the another.

Introduction to Software

Software is a set of instructions, information, or computer programs that are used to run devices and perform certain tasks. Hardware, which is a term for a computer's external devices, is the opposite of it. In this usage, "Software" refers to the running scripts, programs, and apps on a device.

Early software was created for certain machines and sold alongside the hardware those computers used. Software started to be marketed on floppy discs in the 1980s, and then on CDs and DVDs. Most software is now bought and downloaded simply from the internet. Websites for vendors or application service providers may contain software.

The following are the most typical types of software among the numerous categories

• Software for applications

• Software for systems

• Software for drivers

• Middleware

• software for programming

Introduction to conda

Most of the tools we want to use in bioinformatics can be installed using Conda, a package, and an environment manager. Not everything is available, but practically everything we're likely to want to use is. Being "conda-installable" indicates that someone (maybe the developer, could be others) has gone through the bother of making it that way. Conda's additional benefit of handling various contexts for us extremely well goes hand in hand with making things simpler to set up. Program A may occasionally be dependent on a particular version of Program B. Then, though, Program C will be dependent on a different version of Program B, which leads to issues.

Conda automatically checks for us when we try to install something new and makes it simple for us to set up and manage distinct environments to prevent these kinds of version conflicts (so we find out now before we break something somewhere under the hood and have no idea what happened). Further advantages include aiding in reproducibility as well, so let's get started!

Management of Software using Conda

When using the Anaconda Prompt in Windows or a terminal window in macOS or Linux, you can use the robust package manager and environment manager known as Conda.

Environment Management

Conda enables you to build independent environments with files, packages, and their dependencies that don't communicate with one another.

You already have a base-named default environment when you start using conda. However, you shouldn't add any apps to your default environment. In order to keep your programs distinct from one another, create independent environments.

Let’s see some of the steps to set up an environment in conda

First, we have to create an environment then we can move to install a package in it. Commands that are used to create a conda environment and install the new packet are

conda create -- name enviorment_name pakage_name

Here environment_name is the name we want to give the conda environment and the pakage_name is the name of the package we want to install.

To use the conda environment, we have to activate it which can be done in two methods based on the versions

• For the versions which are prior to 4.6 the commands are

Windows: activate environment_name
macOS and Linux: source activate environment_name

• For version 4.6 and later versions, the commands are

Windows: conda activate environment_name
macOS and Linux: conda activate environment_name

To get the list of all the environments that are created by the user the following tag could be used

conda info –envs

If the user only put the command “activate or source activate” then the current environment will be deactivated and the user will revert back to the base environment.

Managing Python

Python can be easily installed and used with the help of the conda, conda installs the python version which is the same as you had used when you installed the Anaconda. It also provides the option to download a different version of python which the user needs.

Let’s see some of the commands which can be used to manage the python programming language

• First, we have to create an environment then we will install a special version of python in it

  conda create -- name enviorment_name python = x
  

  Here environment_name is the name we want to give the conda environment and x is the version of python that we want to install.

• To use python first we have to activate the conda environment then we can move with it.

• Also to verify whether the current version is activated or not we can use the above-defined third step.

Managing Packages

We have seen how to create the environments and install the packages in them, but the last task is how to manage the packages that we have installed. There are various commands that are provided by the conda with the help of which we can find a package or find all the packages which we have in the current environment.

To search a package − ‘conda search package_name’ and to find all the packages in the environment ‘conda list’ commands are used where the ‘package_name’ is the name of the particular package we want to search.

Conclusion

Conda is an environment and package manager which is the best and the easiest of all the competitors available in the market. The majority of the tools we want to use in bioinformatics can be installed using Conda, a package, and an environment manager. Not everything is available, but practically everything we're likely to want to use is.

Being "conda-installable" indicates that someone (maybe the developer, could be others) has gone through the bother of making it that way.