Add draft installation and usage instructions

README.md

@@ -6,10 +6,20 @@ It is based off of the original code and research from the Berger Lab stored in
 
 ## Prerequisites
 
-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:
+pgmap requires python3 above or equal to version 3.10
 
+### Installation using pip
 
-At this time, pgmap is not yet published to PyPI. But can be used following these steps:
+```
+pip install pgmap
+```
+
+Check if pgmap is installed in path:
+```
+pgmap --help
+```
+
+### Installation from source code
 
 First you can clone this repo:
 ```
@@ -23,7 +33,17 @@ pip install -r requirements.txt
 
 Now you can install the package
 ```
-python3 -m pip install .
+pip install .
+```
+
+Run tests to verify pgmap is running
+```
+python3 -m tests
+```
+
+Check if pgmap is installed in path:
+```
+pgmap --help
 ```
 
 ## Getting Started
@@ -35,3 +55,8 @@ You'll need to declare four files (we have example data to work with):
   - R1 fastq file
 - barcodes path which says which barcodes go to which cells
 - pgPEN annotations path (this is included in the package)
+
+Usage example (test data available in `example-data`)
+```
+pgmap --fastq example-data/two-read-strategy/240123_VH01189_224_AAFGFNYM5/Undetermined_S0_R1_001_Sampled10k.fastq.gz example-data/two-read-strategy/240123_VH01189_224_AAFGFNYM5/Undetermined_S0_I1_001_Sampled10k.fastq.gz --library example-data/pgPEN-library/paralog_pgRNA_annotations.txt --barcodes example-data/two-read-strategy/240123_VH01189_224_AAFGFNYM5/barcode_ref_file_revcomp.txt --trim-strategy two-read
+```