Cannot install cLoops2 as instructed about cloops2

[CharlsW2023]

I then modify the cLoops2_env.yaml to not request pip install cLoops2==1.0.0 version (remove ==1.0.0) and run
$ conda create -n cLoops2-2 python=3.7
$ conda activate cLoops2-2
$ conda env update --file cLoops2_env.yaml

The error shows:

Pip subprocess error:
ERROR: Package 'SciPy' requires a different Python: 3.7.0 not in '>=3.8,<3.11'

failed

[YaqiangCao]

I then modify the cLoops2_env.yaml to not request pip install cLoops2==1.0.0 version (remove ==1.0.0) and run $ conda create -n cLoops2-2 python=3.7 $ conda activate cLoops2-2 $ conda env update --file cLoops2_env.yaml

The error shows:

Pip subprocess error: ERROR: Package 'SciPy' requires a different Python: 3.7.0 not in '>=3.8,<3.11'

failed

Hi Charles,
Sorry for the late reply. Have you solved the problem?
I could recommend you to install the following 3rd dependencies with conda or pip, then in the cLoops2 directory run python setup.py install to install it.

tqdm
numpy 
scipy 
pandas
sklearn
seaborn
pyBigWig
matplotlib
joblib
networkx

Best,
Yaqiang

[CW20221031]

Hi Yaqiang,

Thank you for your reply!

I found the issue and solved it now. The issue is that I added "module load Bowtie2" in my .bashrc to load the pre-installed Bowtie2 module from our cluster, which would auto-load Python3.10 from our cluster. And this is conflicted with my conda environment. Especially if the packages I want to install in my conda environment already exist in our cluster's Python3.10 directory, it would display Requirement already satisfied: xxx package in our cluster's Python3.10 directory. But it cannot actually use these packages (I don't know why) when running cLoops2.

To solve this, I need to run "module purge" first to remove all modules I loaded. And then run pip install cLoops2 in my conda environment. I have done debugging for several days and found the issue. Glad it works!

Best,
Charles