Ghana-Installation-software.md

@@ -75,12 +75,14 @@ bam-readcount does not support in source builds. Create a new build directory, e
       cd bam-readcount
       mkdir build
       cd build        
-      cmake /path/to/bam-readcount/
+      cmake ..
       make
+      cd ..
+      cp  -r bam-readcount /usr/local
 
-Add /usr/local/bam-readcount/build/bin to the path :
+Add /usr/local/bioinfo/bam-readcount/build/bin to the path :
 
-       echo  'export PATH=/usr/local/bam-readcount/bin:$PATH' >>/etc/profile
+       echo  'export PATH=/usr/local/bioinfo/bam-readcount/bin:$PATH' >>/etc/profile
        source /etc/profile
 
 ### Usage :
@@ -97,13 +99,13 @@ URL: http://www.girinst.org/censor/
    
        tar xvfz censor-4.x.x.tar.gz
        cd censor-4.x.x
-       ./configure prefix=/usr/local/censor-4.x.x
+       ./configure prefix=/usr/local/bioinfo/censor-4.x.x
        make
        make install
 
-Add /usr/local/censor-4.x.X to the path :
+Add /usr/local/bioinfo/censor-4.x.X to the path :
 
-       echo  'export PATH=/usr/local/censor-4.x.x:$PATH' >>/etc/profile
+       echo  'export PATH=/usr/local/bioinfo/censor-4.x.x:$PATH' >>/etc/profile
        source /etc/profile
 
 
@@ -118,11 +120,11 @@ URL: https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/
 
          wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip
          unzip bowtie2-2.3.4.3-linux-x86_64.zip
-         cp bowtie2-2.3.4.3-linux-x86_64 /usr/local/bowtie2-2.3.4.3
+         cp bowtie2-2.3.4.3-linux-x86_64 /usr/local/bioinfo/bowtie2-2.3.4.3
          
-Add /usr/local/bowtie2-2.3.4.3 to the path :
+Add /usr/local/bioinfo/bowtie2-2.3.4.3 to the path :
 
-       echo  'export PATH=/usr/local/bowtie2-2.3.4.3:$PATH' >>/etc/profile
+       echo  'export PATH=/usr/local/bioinfo/bowtie2-2.3.4.3:$PATH' >>/etc/profile
        source /etc/profile
 
 ### Usage:
@@ -143,13 +145,13 @@ URL: https://ccb.jhu.edu/software/tophat/index.shtml
          wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
          tar xvfz tophat-2.1.1.tar.gz 
          cd tophat-2.1.1
-         ./configure --prefix=/usr/local/tophat-2.1.1
+         ./configure --prefix=/usr/local/bioinfo/tophat-2.1.1
          make 
          make install
                  
-Add /usr/local/tophat-2.1.1 to the path :
+Add /usr/local/bioinfo/tophat-2.1.1 to the path :
 
-       echo  'export PATH=/usr/local/tophat-2.1.1:$PATH' >>/etc/profile
+       echo  'export PATH=/usr/local/bioinfo/tophat-2.1.1:$PATH' >>/etc/profile
        source /etc/profile
 
 ### Usage: