Ghana-Installation-software.md

@@ -467,10 +467,9 @@ URL: https://www.r-project.org/
         wget https://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
         tar xvfz R-3.5.1.tar.gz
         cd R-3.2.2
-$~ ./configure –with-x=no --with-lapack --with-blas --enable-R-shlib --prefix= /usr/local/bioinfo/R-3.5.1
-
-$~ make -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.101-2.6.6.1.el7_2.x86_64/include/
-$~ make install 
+        ./configure –with-x=no --with-lapack --with-blas --enable-R-shlib --prefix= /usr/local/bioinfo/R-3.5.1
+        make -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.101-2.6.6.1.el7_2.x86_64/include/
+        make install 
 
         
 
@@ -487,3 +486,69 @@ Add these variables to the path :
           
             R to enter the console
             install.packages("package_to_install")  # command to install a R package
+
+# SPAdes:
+
+Description: SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
+
+
+URL: http://spades.bioinf.spbau.ru/release3.10.1/manual.html#sec2.1
+
+
+### Installation:
+
+            cd /usr/local/bioinfo
+            wget http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1-Linux.tar.gz
+            tar -xzf SPAdes-3.10.1-Linux.tar.gz
+            mv SPAdes-3.10.1-Linux SPAdes-3.10.1
+
+        
+
+Add this variable to the path :
+
+       echo  'export PATH=/usr/local/bioinfo/SPAdes-3.10.1/bin/:$PATH' >>/etc/profile
+       
+
+       source /etc/profile
+
+
+### Usage:
+          
+            look at the scripts in /usr/local/bioinfo/SPADES-3.10.1/bin
+            python script + arguments
+           
+# AByss:
+
+Description: ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
+
+
+URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss
+
+
+### Installation:
+
+            yum install sqlite
+            yum install sqlite-devel
+            wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.5/abyss-2.1.5.tar.gz
+            tar xvfz abyss-2.1.5.tar.gz
+            cd abyss-2.1.5
+            ./configure –prefix=/usr/local/bioinfo/abyss-2.1.5 --without-sparsehash
+            make
+            make install
+
+
+        
+
+Add this variable to the path :
+
+       echo  'export PATH=/usr/local/bioinfo/abyss-2.1.5/bin/:$PATH' >>/etc/profile
+       
+
+       source /etc/profile
+
+
+### Usage:
+          
+            look at the scripts in /usr/local/bioinfo/SPADES-3.10.1/bin
+            python script + arguments
+