Installation Problem

[H-Qiya]

Hi,
I was trying to run LORALS, but it seemed that I fell into a dead loop.
First I created an independent environment named LORALS in conda, installed samtools as well as bedtools, and ran the code:

python3 setup.py install

It then reported an error:

Traceback (most recent call last):
File "setup.py", line 18, in
from setuptools import setup
ModuleNotFoundError: No module named 'setuptools'

So I installed pip and used pip to install setuotools successfully, and ran the code again:

python3 setup.py install

This time it reported:

Traceback (most recent call last):
File "setup.py", line 82, in
import lorals.scripts as scripts
ModuleNotFoundError: No module named 'lorals'

I wondered that, if the statement "LORALS depends on Python 3, SAMTools, and Bedtools. All other dependencies are installed automatically by pip" is true, why I need to install 'lorals' before running setup.py? Is it a dead loop?
I search again and found this page:

https://lappalainenlab.github.io/lorals/index.html

And I ran the code from it:

pip install git+https://github.com/mojaveazure/lorals.git

Still failed. Then I suddenly noticed that the website might be outdated, and I changed to the following command:

pip install git+https://github.com/LappalainenLab/lorals.git

Failed again :(

Could you please help me with this installation problem? Looking forward to your reply!

[NikoLichi]

Hi there,

I am just another user using LORALS and did the same installation as you. Perhaps you solved this issue already but just in case.
As a suggestion, if you use conda dependencies try to install dependencies from Anaconda. I the past, I had trouble mixing pip and conda dependencies. I suggest you install setuptools from anaconda like:
conda install -c conda-forge setuptools

In my case, conda complained about a g++ and gcc dependencies which I installed using conda. And it seems to be working "fine".

I hope this helps,

All the best,
Niko

[bkcenik]

I'm also just a user - I had similar compiling issues when I was trying to install (on an HPC environment). Using an up to date version of gcc fixed my problem. Our default version is 4.x, I just loaded 11.2.0 and was able to install without issues.