Windows 10 won't install Nextclade CLI

Help and Getting Started
1

I have previously been using Nextclade CLI on Linux with no problems. However, I’m not able to install it on my Windows 10 computer. What happens is that I download the GNU-file for windows but when I try to open it, nothing happens. Same when I try to download via the command line instead. I’ve tried to open the file as an administrator and temporarily deactivated my antivirus software but the result is the same.

Anyone who’s encountered a similar problem with suggestions on how it could be solved?

Thank you
Tomas

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Hi @Tomas,

Windows version is not very well tested and we don’t have much resources to test on all platforms.

In order for us to diagnose this problem, could you please provide exact steps to reproduce the issue, and, if possible, make some screenshots demonstrating it?

As a workaround, Windows users could try to use one of the following:

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Hi Ivan,
Thank you for your response. I managed to solve the issue by downloading the exe-file and then instead of clicking on it,I ran the file in the terminal instead. Nextclade is up and running on my Windows computer now :slight_smile:

Kind regards,
Tomas

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Hi Tomas! Do you mind explaining what you mean by “you ran the file in the terminal”. I am also having similar issues with you. I use Windows.

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@Chidozie This is a very old forum thread, so Tomas might not be able to respond on time, so let me try instead.

Nextclade CLI is a command-line application, which is to be run in a terminal (console) emulator. In Windows there are multiple flavors of terminals available. You could try for example Windows Terminal program from the official Microsoft website: Windows Terminal - Official app in the Microsoft Store. It requires certain amount of knowledge with terminal commands though.

We don’t deal with Windows much here and we recommend to run Nextclade on Linux or macOS where possible, but let me know what problems you’ve encountered (including a list of steps you’ve taken, and the full text of error messages, if you get any) and we’ll try to assist.

If you want a simpler solution, we also have Nextclade Web, which is a web application which does the same thing as Nextclade CLI, but in a friendly interface. For Nextclade Web you only need a web browser. Here is a link to the website: https://clades.nextstrain.org

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For general use, I recommend WSL (mentioned by @ivan-aksamentov previously) which will open the doors to running most bioinformatics command line tools, as the community primarily develops for Unix/Linux systems. Much of the bioinformatics command line support on the internet assumes a Unix/Linux environment.

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@Chidozie I believe what @Tomas was referring to was using the Windows Command Prompt. In Windows terms, Nextclade CLI is a “console app”, to be run from a command prompt. It does not present a Windows UI.

To “install” I download the file nextclade-x86_64-pc-windows-gnu.exe from the Assets section of this page. I usually rename the file to nextclade.exe for simplicity.

Here’s a sample command line I run, to get the latest sars-cov-2 dataset.

nextclade dataset get --name “sars-cov-2” --output-dir “data/sars-cov-2”

HTH

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