The easiest way to install krepp is by using conda

conda install bioconda::krepp 

This will install the latest available version, simply run krepp --help to test.

If the installation fails due to a libcurl-related error, try to switch to an environment with Python <= 3.10.

To compile from the source, clone the repository with its submodules (might take a while) and compile with

git clone --recurse-submodules -j8 https://github.com/bo1929/krepp.git
cd krepp && make

and run ./krepp --help. Then, perhaps, copy it to a directory you have in your $PATH (e.g., cp ./krepp ~/.local/bin).

• The makefile is supposed to detect if you have libcurl and OpenMP available on your machine and compile accordingly.
• If krepp is compiled without libcurl, you won't be able to give FTP URLs instead of paths in your commands or input files.
• You can install it via sudo apt install curl. This enables the use of URLs instead of paths and retrieves FASTA/FASTQ files from FTP servers (e.g., NCBI), allowing gzip-compressed files as well.
• If OpenMP is not available on your machine, you won't be able to benefit from parallel processing, but you can still compile krepp. For installing/configuring OpenMP on macOS, you might find this useful.
• krepp is optimized for x86-64 CPU architecture, but can still be used on ARM CPUs.
• If you would like to use another compiler which is on your path, specify it via the COMPILER variable when running make (e.g., make COMPILER=g++-14).