From 3e6a35b6dfec2af8700711ac78960f2ec3c94c8a Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Fri, 16 Sep 2016 09:04:26 +0100
Subject: [PATCH 1/3] Makes cpu check work on osx, next try to get homebrew
 gnutil to link

---
 setup.sh | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/setup.sh b/setup.sh
index bd83b23..7c2b989 100755
--- a/setup.sh
+++ b/setup.sh
@@ -65,23 +65,29 @@ get_file () {
   fi
 }
 
-set -e
-
 if [ "$#" -ne "1" ] ; then
   echo "Please provide an installation path  such as /opt/ICGC"
   exit 0
 fi
 
-CPU=`grep -c ^processor /proc/cpuinfo`
+CPU=1
+ls /proc/cpuinfo >& /dev/null # very noddy attempt to figure out thread count
 if [ $? -eq 0 ]; then
-  if [ "$CPU" -gt "6" ]; then
-    CPU=6
-  fi
+  CPU=`grep -c ^processor /proc/cpuinfo`
 else
-  CPU=1
+  CPU=`sysctl -a | grep machdep.cpu | grep thread_count | awk '{print $2}'`
+  if [ $? -ne 0 ]; then
+    # fall back to unthreaded core test
+    CPU=`sysctl -a | grep machdep.cpu | grep core_count | awk '{print $2}'`
+  fi
+fi
+if [ "$CPU" -gt "6" ]; then
+  CPU=6
 fi
 echo "Max compilation CPUs set to $CPU"
 
+set -e
+
 INST_PATH=$1
 
 # get current directory

From 3ba80051627181444092d092294257f93c60e4ab Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Sep 2016 09:38:24 +0100
Subject: [PATCH 2/3] Changes to setup.sh to allow CPU checking in OSX

---
 CHANGES.md  | 9 ++++++---
 VERSION.txt | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 9168c29..01900ed 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,8 +1,11 @@
-###0.2.1
+### 0.3.0
+* Changes to setup.sh to permit OSX installation
+
+### 0.2.1
 * Corrections to logic
 
-###0.2.0
+### 0.2.0
 * Added bedgraph to bw functionality via bg2bw
 
-###0.1.0
+### 0.1.0
 * First release
\ No newline at end of file
diff --git a/VERSION.txt b/VERSION.txt
index 0c62199..0d91a54 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-0.2.1
+0.3.0

From 1fbc9d38b17b60924e37c890ba94d742e6758cbc Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Tue, 27 Sep 2016 09:40:34 +0100
Subject: [PATCH 3/3] Added information on OSX installation

---
 INSTALL.md | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index 27cfcd8..0bce608 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -12,8 +12,6 @@ setup.sh will install
 #Other Software
   For installation to proceed you require the following packages:
 
-
-
 ##For Ubuntu (tested with 14.04)
 ```
 apt-get update && \
@@ -46,3 +44,20 @@ sudo make install && \
 cd .. && \
 rm -rf nettle nettle.tar.gz
 ```
+
+##OSX
+  In order for cgpBigWig to install you may need the following packages installed
+```
+brew install gnutls
+# fixes gnutls include
+export LIBRARY_PATH="$HOME/homebrew/lib"
+export LDFLAGS="-L$HOME/homebrew/opt/libffi/lib"
+export PKG_CONFIG_PATH="$HOME/homebrew/opt/libffi/lib/pkgconfig"
+brew install libffi
+# from https://p11-glue.freedesktop.org/doc/p11-kit/devel-building.html
+wget https://p11-glue.freedesktop.org/releases/p11-kit-0.23.2.tar.gz
+tar zxf p11-kit-0.23.2.tar.gz
+cd p11-kit-0.23.2
+./configure --prefix=$HOME/local --without-trust-paths
+make
+```
\ No newline at end of file