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conda/mamba install #10

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auberginekenobi opened this issue Jun 11, 2024 · 1 comment
Open

conda/mamba install #10

auberginekenobi opened this issue Jun 11, 2024 · 1 comment

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@auberginekenobi
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Hi team, exciting work!
I'd like to suggest including instructions for installing dependencies with conda/mamba instead of pip. This circumvents 2 issues I encountered during installation:

The only code change would be in the requirements.txt file:

(coral) ochapman@pines:~/CoRAL$ diff conda-requirements.txt requirements.txt 
3c3
< gurobi
---
> gurobipy
9c9
< bioconductor-dnacopy
---
> 

N.B. that the following channels are required:

(coral) ochapman@pines:~/CoRAL$ conda config --show channels
channels:
  - conda-forge
  - bioconda
  - gurobi
@MJoseMo
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MJoseMo commented Jul 16, 2024

Hi, I have encountered problems in installing the packages from the requirement.txt file.

I have solved it with the commands listed on the link: etal/cnvkit#890

pip uninstall cython numpy -y
pip install cython==0.29.17 numpy==1.26.4 -y
git clone -b v0.14.9 --single-branch https://github.com/tiwalayo/pomegranate.git
pip install -e pomegranate/

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