Installation problem
Closed this issue · 2 comments
Hi, there:
I'd installed liftoff a few months ago using
conda install -c bioconda minimap2
git clone https://github.com/agshumate/Liftoff liftoff
cd liftoff
python setup.py install --user
from the old instructions, and it worked perfectly, except I had to run python liftoff.py instead of just liftoff to get the program to run.
For various reasons, I had to delete and reinstall liftoff the other day in a new conda environment, but when I tried to re-install with the previous commands, I got various reports that
Requirement already satisfied: liftoff in /path/to/home/directory/.local/lib/python3.6/site-packages/Liftoff-1.4.2-py3.6.egg
etc, which I think is ok, but I didn't get a liftoff.py file, and just running liftoff -h in the liftoff directory to test the code produced the errorliftoff: command not found. Same thing happened when I installed with pip install liftoff. When I tried to install liftoff with conda in a new conda environment with the updated command from the liftoff github
conda install -c bioconda liftoff
I got the error
UnsatisfiableError: The following specifications were found to be incompatible with each other
Package python conflicts for:
liftoff -> python[version='>=3']
Package biopython conflicts for:
liftoff -> biopython[version='>=1.76']
Package gffutils conflicts for:
liftoff -> gffutils[version='>=0.10.1']
Package numpy conflicts for:
liftoff -> numpy[version='>=1.19.0']
Package minimap2 conflicts for:
liftoff -> minimap2
Package networkx conflicts for:
liftoff -> networkx[version='>=2.4']
Package pysam conflicts for:
liftoff -> pysam[version='>=0.16.0.1']
Package pyfaidx conflicts for:
liftoff -> pyfaidx[version='>=0.5.8']
Package interlap conflicts for:
liftoff -> interlap[version='>=0.2.6']
even though my conda environment is python 3.6. The bottom line is that no installation is working, and I was having no problems installing and running it a few months ago. Not sure what to do. I'm on an HPC compute cluster if that helps.
Liftoff is an excellent tool, by the way; it's become essential to my work, so I'm quite anxious to get it running again! Thanks.
Hi, it's me again: I found out that /liftoff/run_liftoff.py replaces liftoff.py in the most recent version of liftoff. So I'm able to use that to run it and it works fine. Not sure if you want to address the installation issues I mentioned previously, it's up to you. (Also, liftoff seems like it's crazy faster now.) Thank you!
Hi there,
I'm glad you got it working! The installation issues above may be specific to your environment, perhaps due to the fact that two different versions were installed. The error 'Requirement already satisfied: liftoff in /path/to/home/directory/.local/lib/python3.6/site-packages/Liftoff-1.4.2-py3.6.egg' is what suggests that it is maybe due to installing it twice although I can't say for sure without doing some more digging. But since you got it working I am going to go ahead and close this issue