Merge pull request #17 from FredHutch/cansavvy/requirements

Update requirements.txt

.github/workflows/test-package.yml

@@ -12,16 +12,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["pypy3.10", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["pypy3.10", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      # You can test your matrix by printing the current Python version
+
       - name: Display Python version
         run: |
           python -c "import sys; print(sys.version)"
+          pip install -r requirements.txt
           python3 -m pip install . && python3 -m tests

README.md

@@ -8,10 +8,30 @@ It is based off of the original code and research from the Berger Lab stored in
 
 In order to run this pipeline you will need R and to install the `pgmap` package and its dependencies. In R you can run this to install the package:
 
-TODO: installation instructions
 
-## Getting Started Tutorial
+At this time, pgmap is not yet published to PyPI. But can be used following these steps:
 
-Now you can [go to our tutorial to get started!](https://fredhutch.github.io/pgmap/articles/getting_started.html)
+First you can clone this repo:
+```
+git clone https://github.com/FredHutch/pgmap
+```
 
-Follow the steps there that will walk you through the example data. Then you can tailor that tutorial to use your own data.
+To install required dependencies:
+```
+pip install -r requirements.txt
+```
+
+Now you can install the package
+```
+python3 -m pip install .
+```
+
+## Getting Started
+
+You'll need to declare four files (we have example data to work with):
+
+- Two sequencing reads files:
+  - I1 fastq file
+  - R1 fastq file
+- barcodes path which says which barcodes go to which cells
+- pgPEN annotations path (this is included in the package)

requirements.txt

@@ -0,0 +1,3 @@
+biopython==1.85
+python-Levenshtein==0.26.1
+setuptools==75.1.0