./updateTaxonomy.sh: line 287: make: command not found

[transyhieu]

I was trying to use both 2.8 and 2.8.1, but both of them showed the error. I run the command on a conda environment, I was also asked to install curl, but nothing works after installing curl. Thank you and have a nice day Hieu

[clementmlay]

I have the same problem

[danchurch]

Is make available to you in the environment you are using (i.e. are you on some sort of cluster or cloud virtual machine where make isn't installed or within your user-privileges?)

For me, I am able to install make (as in, with an ubuntu environment: sudo apt install make), and CCMetagen can then use it, getting rid of the error.

[FranciscoAscue]

If you're using Anaconda, you'll need to run ktUpdateTaxonomy.sh in your environment. The same goes for Miniconda you may need to create two folders, taxonomy and scripts, in the '~/miniconda3/envs/krona_env/bin' directory. This is what I did, and then I linked the scripts and content from the ~/miniconda3/envs/krona_env/opt/krona/scripts folder ln -s ~/miniconda3/envs/krona_env/opt/krona/scripts/taxonomy.make . ln -s ~/miniconda3/envs/krona_env/opt/krona/scripts/extractTaxonomy.pl .. Finally, run ktUpdateTaxonomy to complete the process. – if you encounter an error. navigate to cd ~/miniconda3/envs/krona_env/opt/krona/taxonomy/ and run ./updateTaxonomy.sh. This will update the taxonomy and resolve the issues.

It's possible that linking the content of the scripts and taxonomy folders may not be necessary, but I haven't been able to verify this. If anyone has tested this and found success without linking the folders, that would be great to know.