agshumate/Liftoff

Trouble with installation

Opened this issue · 1 comments

danatlin commented

Hi,
I am trying to follow the instruction to install liftoff but kept running into issues.
Specifically I can't make Conda to recognize minimap2/mappy.
When I did Conda install minimap2, it said no package was found; it seems like it has become mappy on bioconda.
While I could install mappy with no problem.
When I run Conda install liftoff, it still says minimap2 is not installed.
When I checked Conda list, there was only mappy; When I looked into $path_to_envs/lift_env/bin, I could see both mappy and minimap2.py.
I honestly don't know wheat I did wrong.

Thanks,
Dana

haydenji0731 commented

What happens if you try running minimap within your conda env? Mappy is a python wrapper for minimap2, and it doesn't substitute minimap2 needed for running LiftOff. I would try to download the precompiled binary for minimap2 and export that path within your env so that LiftOff can system call minimap2.