Help on getting started with the nextclade CLI


I’m attempting to set up the nextclade CLI on a linux computer that I can ssh to from a windows PC to run my analyses. However, the documentation is fairly cryptic with respect to installation. I have attempted both manual and command-line downloads from here.

I’m not sure how to get from the downloaded shared library file to start using the nextclade commands. I haven’t found an application yet that is able to open the downloaded nextclade file (I’m not even sure I’m supposed to open it :stuck_out_tongue: )

Any time I enter nextclade --help in that folder, I get a nextclade: command not found error; and bash will not open the file, and to my knowledge I’m not even in a nextclade-specific environment.

Ultimately, I’m hoping for a bit more clear instructions on steps to take after the download step. Additionally, what commands can I use to make sure my local nextclade CLI is up to date before I run my analyses? Your help is greatly appreciated!

Thank you for your time,

Hi Jonathan,

to download, this should do the trick:

curl -fsSL "" -o "nextclade" && chmod +x nextclade

this should download the binary. This binary needs to go to a place in your $PATH, or you can call it with the full path to the binary.

try ./nextclade --help


1 Like

Thank you so much! Something so simple and I couldn’t wrap my head around it for some reason

People coming from Windows usually have to learn that on Linux they need to specify explicit paths to executables that located in current dir, e.g. ./nextclade, and such files need to be marked as executable, e.g. chmod +x nextclade.

For me is the best way to distribute the latest software on Linux and Mac, but that needs additional one time setup, on both client side and in release pipeline.