Help on getting started with the nextclade CLI

Help and Getting Started
1

Hello,

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,
Jonathan

2

Hi Jonathan,

to download, this should do the trick:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-Linux-x86_64" -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

best,
richard

1 Like
3

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

4

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 https://brew.sh/ 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.