Linux Terminal vs PyCharm Terminal

Question

[tsomakiank]

Hello to everyone! I am new to bioinformatics and I have a question. The first thing that was suggested to do from several tutorials in order to do bioinformatics was to install a linux distro to work on and use the bash terminal. I installed ubuntu and I also installed pycharm for python. Then I realized that Pycharm also offers a bash terminal. My question is why I need to install linux rather than just install Pycharm in a windows machine and run the analyses on the terminal offered by pycharm. I am new to the field, so I hope my question makes sense.

Answer 1

[Mensur Dlakic]

You don't need to do anything. Your question, like many others on this forum, is about the tools. Different people can finish the same job using the same or different tools. Editing python scripts can be done in PyCharm in a way that may be more convenient than doing it in plain Linux shell. Just like bioinformatics can be done within Windows environment. However, I think most people will agree that doing serious bioinformatics is likely to be more comfortable in Linux than in Windows environment. There are many reasons for that, starting with directory and file names, end of line issues, support for automatic package installation, resource overhead, etc.

A concise answer to your question is that it may be easier to work with python scripts using PyCharm under Windows, but in the long run bioinformatics is easier to do with Linux.

[tsomakiank]

I got your point and seems very reasonable! Thanks a lot Mensur for your help!

Answer 2

[GenoMax]

From https://www.jetbrains.com/help/pycharm/terminal-emulator.html

PyCharm includes an embedded terminal emulator for working with your command-line shell from inside the IDE.

At first glance that seems to indicate that one would still need an underlying OS/Shell. So very likely you can't simply use the pyrcharm terminal as a replacement for full linux OS.

[tsomakiank]

Riiiight, that makes sense now. Thanks a lot GenoMax !