conda/mamba install

[auberginekenobi]

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:

• For some reason, the grbgetkey utility is included in the gurobi package on conda but not the gurobipy package on pip. This utility seems to be required to install a gurobi license. See also https://support.gurobi.com/hc/en-us/articles/360044290292-How-do-I-install-Gurobi-for-Python .
• conda/mamba can install the bioconductor-dnacopy dependency.

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]

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/

[madagiurgiu25]

Hi together,

I have encountered similar issue. I think one issue if cnvkit installation. The cnvkit==0.9.11 did not installed successfully. However, what it worked was installing with pip (using python=3.9):

• cnvkit==0.9.10
• numpy==1.24.2
• pandas==1.5.3
• pandas-datareader==0.10.0