make: *** src: No such file or directory. Stop.

[lauraelf]

I am attempting to install Kraken2 onto my linux system into the folIowing directory /usr/local/bin/kraken2

have both the "install_kraken2.sh" and the source code kraken2-2.1.3.tar.gz inside the directory and the pwd is also this same directory. When I run the script
sudo ./install_kraken2.sh /usr/local/bin/kraken2

I get the following error
make: *** src: No such file or directory. Stop

I saw this error in another closed thread, however the cause was not having the source code downloaded. I do have the source code downloaded as stated above, so it is a different issue. How can I get Kraken to install

[ChillarAnand]

$ sudo ./install_kraken2.sh /usr/local/bin/

Run this command. /usr/local/bin/kraken2 - this path itself is missing and it is failing to build.

[lauraelf]

Okay, however the directory does exist, I created the directory and navigated to it and placed the files all inside it before trying to install. I also tried doing the suggestion and running "/usr/local/bin/kraken2" and the result (see below) is the same error

blastkid@blastkid-Super-Server:/usr/local/bin/kraken2$ /usr/local/bin/kraken2
-bash: /usr/local/bin/kraken2: Is a directory
blastkid@blastkid-Super-Server:/usr/local/bin/kraken2$ sudo ./install_kraken2.sh /usr/local/bin/kraken2
make: *** src: No such file or directory. Stop.
blastkid@blastkid-Super-Server:/usr/local/bin/kraken2$

[ChillarAnand]

Try running these commands as is without any modifications.

cd
mkdir -p /usr/local/bin
export PATH=/usr/local/bin/:$PATH

git clone https://github.com/DerrickWood/kraken2/
cd kraken2
sudo ./install_kraken2.sh /usr/local/bin/

kraken2 --help

There are alternate ways to install kraken. You can use conda or brew as well.

https://avilpage.com/2024/07/mastering-kraken2-initial-runs.html