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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
51 stars 13 forks source link

conda install: pip failed, No matching distribution found for codecov==2.1.12 #241

Closed ShannonTown closed 1 year ago

ShannonTown commented 1 year ago

Hi, I ran into the following error when trying to install pepatac using conda. It seems that codecov package has been removed from PyPi as deprecated. How to bypass this if I still want to use conda? Thank you!

Installing pip dependencies: \ Ran pip subprocess with arguments: ['/*****/miniconda3/envs/pepatac/bin/python', '-m', 'pip', 'install', '-U', '-r', '/**/pepatac/condaenv.og390thz.requirements.txt'] Pip subprocess output: Collecting bio==1.3.2 Downloading bio-1.3.2-py3-none-any.whl (272 kB) Collecting biopython==1.79 Downloading biopython-1.79-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB) Collecting biothings-client==0.2.6 Downloading biothings_client-0.2.6-py2.py3-none-any.whl (37 kB) Collecting certifi==2021.10.8 Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting charset-normalizer==2.0.7 Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB)

Pip subprocess error: ERROR: Could not find a version that satisfies the requirement codecov==2.1.12 (from versions: 2.1.13) ERROR: No matching distribution found for codecov==2.1.12 failed

CondaEnvException: Pip failed

ayobi commented 1 year ago

Hi @ShannonTown, you should be able to install pepatac using conda now :+1:

Ruthwww commented 11 months ago

Hi @ShannonTown, you should be able to install pepatac using conda now 👍

Could u tell me how to do it? u mean using conda install to directly download the PEATAC?

ShannonTown commented 11 months ago

@Ruthwww Here is how I was planning to do it: http://pepatac.databio.org/en/latest/run-conda/

@ayobi Thank you very much! I didn't have a chance to actually try installing pepatac using conda in the end, because I already installed all required packages manually in the conda environment before hearing from you, and passed the "confirm installation" using ./checkinstall. I was able to run the pipeline, except that the "peak_chromosome_distribution" and "peak_TSS_distribution" plots are empty. Is there a quick solution to this issue without reinstalling pepatac from scratch using conda?