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Add yml file and easier installation instruction #125

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Aug 6, 2024
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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ SCICoNE takes a read counts matrix of cells by genomic bins and outputs the copy
## Installation
Once the requirements are in place, downloading and installing SCICoNE takes about 5 minutes.
```bash
git clone git@github.com:cbg-ethz/SCICoNE.git # Clone the repository
git clone https://github.com/cbg-ethz/SCICoNE.git # Clone the repository
cd SCICoNE
mkdir build && cd build # Create and enter the build directory
cmake ../scicone/ # Compile the program with cmake
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61 changes: 23 additions & 38 deletions docs/notebooks/tutorial.ipynb

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19 changes: 19 additions & 0 deletions pyscicone/environment.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
name: Scicone
channels:
- defaults
dependencies:
- python
- ipykernel
- numpy
- scipy
- h5py
- tqdm
- seaborn
- graphviz
- pygraphviz
- conda-forge::matplotlib=3.3.2

- pip
- pip:
- git+https://github.com/cbg-ethz/SCICoNE.git@master#egg=scicone&subdirectory=pyscicone
#pip install pyscicone/
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