You will know if it needs to be added if you see the following message kneaddata: command not found when trying to run KneadData after installing with the “–user” option. Please note when using the “–user” install option on some platforms, you might need to add ‘$HOME/.local/bin/’ to your $PATH as it might not be included by default. This will install the python package into subdirectories of ‘$HOME/.local/’. If you do not have write permissions to ‘/usr/lib/’, then add the option “–user” to the install command.To bypass the install of dependencies, add the option “”–install-option=’–bypass-dependencies-install'”. This command will automatically install Trimmomatic and Bowtie2.At the end of the installation, add the location of the java executable to your $PATH. Then follow the instructions for your platform: Linux 64-bit or Mac OS. First download the JRE for your platform. Before installing KneadData, please install the Java Runtime Environment (JRE).
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