Liftoff pip install fails

[aravindpad]

Hello, I'm trying to configure Liftoff as a module for HPC Enviroment.

As per the setup.py liftoff needs pysam>=0.19.1

import setuptools


setuptools.setup(
	name="Liftoff",
	version="1.6.3",
	author="Alaina Shumate",
	author_email="[email protected]",
	description="A gene annotation mapping tool",
	url="https://github.com/ashumate/Liftoff",
	install_requires=['numpy>=1.22.0', 'biopython>=1.76', 'gffutils>=0.10.1', 'networkx>=2.4', 'pysam>=0.19.1','pyfaidx>=0.5.8','interlap>=0.2.6', "ujson>=3.2.0","parasail>=1.2.1"],
	python_requires='>=3.6',
	packages=['liftoff'],
	entry_points={'console_scripts': ['liftoff = liftoff.run_liftoff:main'], },
)

However, with PIP install I'm getting the following error

Collecting networkx==2.4
  Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
ERROR: Cannot install liftoff==1.6.3.2 and pysam>=0.16.1 because these package versions have conflicting dependencies.

The conflict is caused by:
    The user requested pysam>=0.16.1
    liftoff 1.6.3.2 depends on pysam==0.16.0.1

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

I have all the dependencies installed and pysam is 0.22.0

pip freeze | grep -i pysam
pysam==0.22.0

How can I get around this? I tried source install as well, but getting importlib.metadata.PackageNotFoundError: No package metadata was found for Liftoff

[zgb963]

Hi, I was having the same issue with installing Liftoff with conda, source, and pip in HPC environment. Creating a conda env and installing from bioconda & conda-forge worked for me

conda create -n <name_of_env> -c bioconda -c conda-forge liftoff