Ghana-Installation-software.md

@@ -13,7 +13,7 @@ Add /usr/local/bioinfo/artemis to the path :
        echo  'export PATH=/usr/local/artemis/:$PATH' >>/etc/profile
        source /etc/profile
 
-###Usage :
+### Usage :
 
 The easiest way to run the program is to run the script called art in the Artemis installation directory, like this:
            
@@ -27,22 +27,31 @@ For other available options use:
            
         art -help
 
-# Artemis :
+# bam-readcount :
+
+The purpose of this program is to generate metrics at single nucleotide positions.
+There are number of metrics generated which can be useful for filtering out false positive calls.
 
-Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
-       URL : http://sanger-pathogens.github.io/Artemis/Artemis/
 ### Installation :
 
-      wget  ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.tar.gz
-      tar xfvz artemis.tar.gz -C /usr/local/bioinfo/
-      chmod -R +x /usr/local/bioinfo/artemis
+    yum groupinstall "Development tools" 
+    yum install zlib-devel ncurses-devel cmake patch
+  
 
-Add /usr/local/bioinfo/artemis to the path :
+#### Clone the bam-readcount repository
+
+        git clone https://github.com/genome/bam-readcount.git
+
+#### Compile bam-readcount
+
+bam-readcount does not support in source builds. Create a new build directory, enter it, and run:
+
+        cmake /path/to/bam-readcount/repo
+        cd /path/to/bam-readcount/repo
+        make
 
-       echo -e « EXPORT PATH=/usr/local/artemis/:$PATH » >>/etc/profile
-       source /etc/profile
 
-###Usage :
+### Usage :
 
 The easiest way to run the program is to run the script called art in the Artemis installation directory, like this: