From a42ff28e6f2b91378972f4bb8c81644b8c8c7701 Mon Sep 17 00:00:00 2001
From: NuttyLogic <colinpfarrell@gmail.com>
Date: Wed, 7 Oct 2020 17:56:04 -0700
Subject: [PATCH] - added support for bedGraph methylation calls

---
 README.md            | 51 ++++++++++++++++++++++++++++++++++++--------
 docs/installation.md | 33 ++++++++++++++++++++++++++--
 setup.py             |  3 +++
 3 files changed, 76 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index a7fa0a6..d836982 100644
--- a/README.md
+++ b/README.md
@@ -14,22 +14,55 @@ BSBolt is released under the MIT license.
 
 BSBolt documentation can be found at [bsbolt.readthedocs.io](https://bsbolt.readthedocs.io).
 
-### Installation
+## Installation
 
-BSBolt alignment is performed using a modified version of [BWA](https://github.com/lh3/bwa). Read simulation is carried 
-out using a modified version of [wgsim](https://github.com/lh3/wgsim). 
+### **PyPi Installation**
 
-
-Install through PyPi
+The easiest installation method is installing pre-compiled binaries using PyPi. Binaries are provided for python >=3.6
+on unix like systems (macOS >=10.15 and linux).
 
 ```shell
 pip3 install BSBolt --user
 ```
 
-Install from source
+### **Installing from Source**
+
+Dependencies
+
+* zlib-devel >= 1.2.3-29
+* GCC >= 8.3.1
+
 ```shell
-git clone git@github.com:NuttyLogic/BSBolt.git
-cd BSBolt-master
-python3 setup.py install .
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd BSBolt
+# compile and install package
+pip3 install .
+```
+
+### **Installing from Source on macOS**
+
+Dependencies 
+* autoconf
+* homebrew
+* xcode
+
+Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, 
+and autoconf are installed. Xcode through the mac App Store, running the xcode installation command listed below, 
+or as part of the [homebrew](https://brew.sh/) macOS package manager installation. The full installation process
+can be completed as outlined below.
+
+```shell script
+# install xcode utilities
+xcode-select --install
+# install homebrew
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
+# install autoconf
+brew install autoconf
+# optionally install python
+brew install python3.8
+# install BSBolt
+pip3 install BSBolt
 ```
 
+
diff --git a/docs/installation.md b/docs/installation.md
index a2f855a..040104f 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -1,5 +1,9 @@
-BSBolt consists of mixture of C, CPP, and Python modules. BSBolt was built to be
-[manylinux2010](https://www.python.org/dev/peps/pep-0571/) compliant.
+BSBolt and dependencies need to be compiled during the installation process. Pre-compiled binaries are available for 
+macOS >= 10.15 and linux distributions released after 2010 according to the 
+[manylinux2010](https://www.python.org/dev/peps/pep-0571/) python enhancement proposal. If a precompiled binary is 
+unavailable for the target OS binaries will be built from source. If working on a linux distribution zlib-devel should 
+be installed prior to compilation. Compilation on macOS requires xcode-command line utilities and autoconf be installed 
+as described below.  
 
 ### **PyPi Installation**
 
@@ -24,3 +28,28 @@ cd BSBolt
 # compile and install package
 pip3 install .
 ```
+
+### **Installing from Source on macOS**
+
+Dependencies 
+* autoconf
+* homebrew
+* xcode
+
+Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, 
+and autoconf are installed. Xcode through the mac App Store, running the xcode installation command listed below, 
+or as part of the [homebrew](https://brew.sh/) macOS package manager installation. The full installation process
+can be completed as outlined below.
+
+```shell script
+# install xcode utilities
+xcode-select --install
+# install homebrew
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
+# install autoconf
+brew install autoconf
+# optionally install python
+brew install python3.8
+# install BSBolt
+pip3 install BSBolt
+```
diff --git a/setup.py b/setup.py
index d8c09f7..4d4a6a7 100644
--- a/setup.py
+++ b/setup.py
@@ -45,6 +45,9 @@ def compile_dependency(compilation_command, cwd):
     for line in iter(comp.stdout.readline, ''):
         formatted_line = line.strip()
         print(formatted_line)
+    for line in iter(comp.stderr.readline, ''):
+        formatted_line = line.strip()
+        print(formatted_line)
 
 
 def make_external_dependencies():