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madagiurgiu25 / decoil-pre

Reconstruct ecDNA from long-read data using Decoil tool
BSD 3-Clause "New" or "Revised" License
7 stars 0 forks source link

Use conda to install Decoil #4

Closed madagiurgiu25 closed 3 months ago

madagiurgiu25 commented 7 months ago

Create a conda installation for Decoil.

zhober commented 5 months ago

When can conda install be available? I really need it. Additionally, I have a new comment in issue.

madagiurgiu25 commented 3 months ago

Dear @zhober,

At the moment I do not have the capacities, but I have now included a installation from source (README.md), which requires conda and pip.

zhober commented 3 months ago

I'm trying to install Decoil from source in Python 3.8. However, I encountered an issue with the pickle5 package, which is only compatible with Python 3.5, 3.6, and 3.7, as mentioned in https://pypi.org/project/pickle5/0.0.11/. Additionally, when attempting to install pybedtools, py2bit, and deeptoolsintervals using pip, I encountered an error message × python setup.py bdist_wheel did not run successfully. But these packages can be installed using conda.

madagiurgiu25 commented 3 months ago

I cannot reproduce your error. I test it now on MacOS 13.1 and it runs successfully. The following steps I performed:

git clone https://github.com/madagiurgiu25/decoil-pre.git
cd  decoil-pre

# create conda environment
mamba env create -f environment.yml
conda activate envdecoil

python -m pip install -r requirements.txt
python setup.py build install

Could you tell me which OS system did you use?

madagiurgiu25 commented 3 months ago

I'm trying to install Decoil from source in Python 3.8. However, I encountered an issue with the pickle5 package, which is only compatible with Python 3.5, 3.6, and 3.7, as mentioned in https://pypi.org/project/pickle5/0.0.11/. Additionally, when attempting to install pybedtools, py2bit, and deeptoolsintervals using pip, I encountered an error message × python setup.py bdist_wheel did not run successfully. But these packages can be installed using conda.

You are right in the documentation is written that pickle5 is compatible with python < 3.8 but for some reason on my MacOS it got installed:

conda activate envdecoil
which python
# <mypath>/miniconda3/envs/envdecoil/bin/python

python -m pip freeze | grep pickle
# pickle5==0.0.11

python
#Python 3.8.0 | packaged by conda-forge | (default, Nov 22 2019, 19:11:19) 
#Type "help", "copyright", "credits" or "license" for more information.
>>>
zhober commented 3 months ago

Could you tell me which OS system did you use?

I install on Linux. It’s strange that you can install pickle5 on python3.8. I can’t find the source for python3.8 in https://pypi.org/project/pickle5/#files for windows Mac or Linux.

madagiurgiu25 commented 3 months ago

I checked the documentation, for Python 3.8 pickle is in the standard library. I have now removed pickle5 this from requirements and let me know if you can now install Decoil from source. Thank you.

madagiurgiu25 commented 3 months ago

@zhober, I will close the issue but please open another one in case you have other questions. Thank you!