added dependencies and their install tips

hcluster_pangenome_matrix.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# 2015 Pablo Vinuesa (1) and Bruno Contreras-Moreira (2):
+# 2015-8 Pablo Vinuesa (1) and Bruno Contreras-Moreira (2):
 # 1: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 # 2: http://www.eead.csic.es/compbio (Laboratory of Computational Biology, EEAD/CSIC, Spain)
 
@@ -46,7 +46,8 @@ function print_notes()
     
     NOTES: 
 
-    $progname is a simple shell wrapper for the ape, cluster and gplots pacakges,
+    $progname is a simple shell wrapper for the ape, cluster and gplots packages,
+    to wich dendextend and factoextra were added later on,
     calling functions to generate different distance matrices to compute distance 
     trees and ordered heatmaps with row dendrograms from the 
     pan_genome_matrix_t0.tab file generated by compare_clusters.pl 
@@ -56,7 +57,7 @@ function print_notes()
     
     i) with root privileges, type the following into your shell console:
        sudo R
-       > install.packages(c("ape", "gplots", "cluster", "factoextra"), dependencies=TRUE)
+       > install.packages(c("ape", "gplots", "cluster", "dendextend", "factoextra"), dependencies=TRUE)
        > q()
        
        $ exit # quit root account
@@ -73,7 +74,7 @@ function print_notes()
        # to make this options persistent
        
        # Call R from your terminal and type:
-       > install.packages(c("ape", "gplots", "cluster"), dependencies=TRUE, lib="~/lib/R") 	
+       > install.packages(c("ape", "gplots", "cluster", "dendextend", "factoextra"), dependencies=TRUE, lib="~/lib/R") 	
    
    iii) Once installed, you can read the documentation for packages and functions by typing the following into the R console:
       library("gplots")       # loads the lib into the environment
@@ -83,7 +84,7 @@ function print_notes()
       help(pdf)               # read about the pdf function, which generates the pdf ouput file     
       ...
      
-   2. The pangenome_matrix ouput file will be automatically edited chagne PATH for Genome in cell 1,1
+   2. The pangenome_matrix ouput file will be automatically edited, changing PATH for Genome in cell 1,1
    
    3. Uses distance methods from the cluster::daisy() function.
    
@@ -98,8 +99,8 @@ function print_notes()
  
    4. For clustering see 
       http://www.statmethods.net/advstats/cluster.html for more details/options on hclust
- 	    http://ecology.msu.montana.edu/labdsv/R/labs/lab13/lab13.html
-     	http://www.instantr.com/2013/02/12/performing-a-cluster-analysis-in-r/
+      http://ecology.msu.montana.edu/labdsv/R/labs/lab13/lab13.html
+      http://www.instantr.com/2013/02/12/performing-a-cluster-analysis-in-r/
 
 NOTES
 
@@ -181,7 +182,7 @@ function print_help()
              goodness of clustering (gap|silhouette width) dentrogram and stats plot.
      
     DEPENDENCIES:
-         R packages: ape, cluster, gplots and factoextra. Run $progname -N for installation instructions.
+         R packages: ape, cluster, gplots, dendextend and factoextra. Run $progname -N for installation instructions.
 	 
     IMPORTANT NOTES: 
         1. to get the best display of your genome lables, these should be made as short as possible.