Ghana-Installation-software.md

@@ -240,3 +240,61 @@ Add /usr/local/bioinfo/hmmer-3.2.1 to the path :
 ### Usage:
           Choose a tool in /usr/local/bioinfo/hmmer-3.2.1/bin
            tool + arguments
+
+
+
+
+# BUSCO:
+
+BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.
+
+URL: https://busco.ezlab.org/
+
+Dependencies: augustus, python3, hmmer
+
+### Installation:
+         
+         mkdir /usr/local/bioinfo/busco-3.0.2
+         cd /usr/local/bioinfo/busco-3.0.2
+         git clone https://gitlab.com/ezlab/busco.git
+         cd busco
+         git checkout 3.0.2
+         python3 setup.py install
+         
+                 
+Add /usr/local/bioinfo/busco-3.0.2/busco/scripts to the path :
+
+       echo  'export PATH=/usr/local/bioinfo/busco-3.0.2/busco/scripts:$PATH' >>/etc/profile
+       source /etc/profile
+
+Copy the config file: 
+
+        cp /usr/local/bioinfo/busco-3.0.2/busco/config/config.ini.defaut /usr/local/bioinfo/busco-3.0.2/busco/scripts/config.ini
+
+Modify the config.ini file with:
+
+        [augustus]
+        # path to augustus
+        path = /usr/local/bioinfo/Augustus-3.3.2/augustus/bin/
+
+        [etraining]
+        # path to augustus etraining
+        path = /usr/local/bioinfo/Augustus-3.3.2/augustus/bin/
+
+        # path to augustus perl scripts, redeclare it for each new script
+        [gff2gbSmallDNA.pl]
+        path = /usr/local/bioinfo/Augustus-3.3.2/augustus/scripts/
+        [new_species.pl]
+        path = /usr/local/bioinfo/Augustus-3.3.2/augustus/scripts/
+        [optimize_augustus.pl]
+        path = /usr/local/bioinfo/Augustus-3.3.2/augustus/scripts
+
+         [hmmsearch]
+         # path to HMMsearch executable
+         path = /usr/local/bioinfo/hmmer-3.2.1/bin
+
+
+### Usage:
+          
+           python3 /usr/local/bioinfo/busco-3.0.2/busco/scripts/run_BUSCP.py + arguments
+           tool + arguments