small commit for v0.1.0

README.md

@@ -1,17 +1,25 @@
-# scrapp
-Species Counting on Reference trees viA Phylogenetic Placements
+# SCRAPP
 
-# Using SCRAPP
+1. **[Introduction](#introduction)**
+2. **[Installation](#installation)**
+3. **[Usage](#usage)**
+4. **[Citing SCRAPP](#citing-scrapp)**
 
-Simple call for a common combination of files, using 4 threads:
+## Introduction
+Species Counting on Reference trees viA Phylogenetic Placements
 
-    ./scrapp.py --jplace epa_result.jplace --alignment query.fasta --threads 4
+## Installation
 
-or with MPI:
+### Through Conda
+```
+conda install -c bioconda scrapp
+```
+Thats it! now you can even skip the remaining installation instructions.
 
-    ./scrapp.py --jplace epa_result.jplace --alignment query.fasta --parallel mpi --threads 4
+### From Source
+
+#### Satisfying Dependencies
 
-# Requirements
 <!-- Required python version:
 
     > 2.7.6 -->
@@ -33,3 +41,24 @@ Then use
     sudo update-alternatives --config mpirun
 
 to configure.
+
+#### Getting the Source
+Perhaps the most robust route to setting up SCRAPP is to do a recursive clone of this github repository:
+```
+git clone --recursive https://github.com/Pbdas/scrapp.git
+```
+
+Alternatively, if the code was downloaded as an archive of the source folder, the setup script _should_ fetch the source tree dependencies automatically (if there is an internet connection).
+
+## Usage
+Simple call for a common combination of files, using 4 threads:
+
+    ./scrapp.py --jplace epa_result.jplace --alignment query.fasta --threads 4
+
+or with MPI:
+
+    ./scrapp.py --jplace epa_result.jplace --alignment query.fasta --parallel mpi --threads 4
+
+## Citing SCRAPP
+
+If you use SCRAPP, please cite the following papers: