Use conda to install Decoil
Closed this issue · 8 comments
Create a conda installation for Decoil.
When can conda install be available? I really need it. Additionally, I have a new comment in issue.
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.
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.
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?
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.
>>>
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.
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.
@zhober, I will close the issue but please open another one in case you have other questions. Thank you!