can not find the installed miniprot

[ikkaku1005]

Hi all,

I am a beginner in bioinformatics and I encountered a problem with the LiftOn command. It cannot find the tool miniprot because I installed miniprot in a different folder, not within the conda environment (since conda didn't work for installing miniprot in my case). How can I define the path for LiftOn to work with the miniprot? The path to my miniprot is "/media/data_01/yucku/SOFTWARE/miniprot" the miniprot command work with the whole path. All other required tools are in the conda environment. The error shows: "miniprot is not installed. Please install miniprot before running LiftOn."

Thank you!

Yu-Chia

[Kuanhao-Chao]

Hi Yu-Chia,

To resolve the issue with the LiftOn command not finding the miniprot tool, you can set the PATH environment variable to include the directory where miniprot is installed. This will allow LiftOn to locate and use miniprot.

You can do this by adding the following line to your shell configuration file (e.g., .bashrc or .bash_profile if you are using bash, or .zshrc if you are using zsh):

export PATH="/media/data_01/yucku/SOFTWARE/miniprot:$PATH"

After adding this line, run the following command to apply the changes:

source ~/.bashrc
# or
source ~/.bash_profile
# or
source ~/.zshrc

This will update your PATH environment variable to include the directory where miniprot is installed, allowing the LiftOn command to find and use miniprot.

If you run the LiftOn command again, it should now be able to locate miniprot and proceed without the "miniprot is not installed" error.

Let me know if you have any other questions!

Kuan-Hao