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Infrastructure and utilities KneadData
34

Thanks for your instruction, bro.

Here I post my solution.

Step One

Create a conda environment for kneaddata.

conda create -n kneaddata

conda activate kneaddata

Step Two

Install python for kneaddata environment.

conda install -n kneaddata python=3.10

Step Three

Clone the latest kneaddata program.

git clone https://github.com/biobakery/kneaddata.git

Step Four

Modify some code lines in the script.

cd kneaddata

Open the setup.py in your editor like vim , nano or visual studio code. and find the function install_trf(final_install_folder, mac_os) (around line 240).

see my underlined url link above
see my underlined url link above1021×807 57 KB

The two URLs are no longer available so we need to replace them manually.

def install_trf(final_install_folder, mac_os):
    """ Download and install trf """

    trf_exe = "trf"

    if mac_os:
        url = "https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.macosx"
    else:
        url = "https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64"

Then, save the changes.

Step Five

Please ensure that you’re in the kneaddata conda environment before running the setup.py script.

python setup.py install

It would take a long time for some users to download the dependencies. You can replace the URL (github, sourceforge) with mirror sites url.

After the installation of dependencies, you can perform the kneaddata pipeline for your metagenomic data successfully now!