Ghana-Installation-software.md

@@ -42,18 +42,38 @@ Dependencies: bamtools, samtools, bfctools, tabix
       tar xfvz 3.3.2.tar.gz -C /usr/local/bioinfo/
       cd /usr/local/bioinfo/Augustus-3.3.2
 
-Modify the following files with the PATH of your bamtools:
+Modify the following file:
       
 `/usr/local/bioinfo/Augustus-3.3.2/auxprogs/bam2hints/Makefile`
 
 with:
 
        INCLUDES = /usr/local/PATH_TO_BAMTOOLS/include
+       LIBS = /usr/local/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz
+
 
 Example:
 
        INCLUDES = /usr/local/bioinfo/bamtools-2.3/include
+       LIBS = /usr/local/bamtools-2.3/lib/libbamtools.a -lz
+
+
+Modify the following file:
+      
+`/usr/local/bioinfo/Augustus-3.3.2/auxprogs/filterBam/src/Makefile`
+
+with:
+
+       BAMTOOLS = /usr/local/PATH_TO_BAMTOOLS/include
+       LIBS = /usr/local/PATH_TO_BAMTOOLS/lib/libbamtools.a -lz
+
+
+Example:
+
+       BAMTOOLS = /usr/local/bioinfo/bamtools-2.3/include
+       LIBS = /usr/local/bamtools-2.3/lib/libbamtools.a -lz
 
+The launch the compilation:
  
       make
       make install