Bug for TRF Download

Infrastructure and utilities KneadData
1

While following the installation instructions for KneadData from the BioBakery GitHub page (GitHub - biobakery/kneaddata: Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.), I encountered an issue during the execution of ‘python setup.py install’. The specific error was related to the inability to download the TRF (Tandem Repeats Finder) software from its specified URL:

Downloading http://tandem.bu.edu/trf/downloads/trf409.linux64
Warning: Unable to download http://tandem.bu.edu/trf/downloads/trf409.linux64
ERROR: Unable to install TRF

Upon inspecting the setup.py file, I noticed that the URL used to download TRF was hard-coded at line 248. To resolve this issue, I visited the TRF GitHub repository under the Releases section at GitHub - Benson-Genomics-Lab/TRF: Tandem Repeats Finder: a program to analyze DNA sequences and obtained the latest URL for the TRF binary, which is https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64.

I then replaced the outdated URL in the setup.py file with the current URL. Additionally, I attempted to access the original URL http://tandem.bu.edu/trf/downloads/trf409.linux64 directly in my browser, but it returned a 404 error, confirming that the link was indeed broken.

2

I also came across a recommendation on the BioBakery forum (ERROR: Unable to find trf - #7 by young_doktor) suggesting the use of a local TRF PATH as a workaround. This approach seems viable for ensuring that the installation process can successfully locate and utilize TRF without relying on an internet download.