Merge pull request #125 from FridljDa/master

Add yml file and easier installation instruction
cbg-ethz · Aug 6, 2024 · 65c247b · 65c247b
2 parents 025a7b7 + d77d4fd
commit 65c247b
Show file tree

Hide file tree

Showing 3 changed files with 43 additions and 39 deletions.
diff --git a/README.md b/README.md
@@ -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

diff --git a/docs/notebooks/tutorial.ipynb b/docs/notebooks/tutorial.ipynb
diff --git a/pyscicone/environment.yml b/pyscicone/environment.yml
@@ -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/