Difference between revisions of "Edwards lab notes"

From MolEvol
(Note updated links!!)
(To install phybase in R on the cluster:)
 
Line 17: Line 17:
 
for each section of the tutorial, cd in the appropriate directory.
 
for each section of the tutorial, cd in the appropriate directory.
  
= To install phybase in R on the cluster: =
+
= To invoke phybase in R on the cluster: =
 
   R
 
   R
 
All commands after the '>' should be entered into R.
 
All commands after the '>' should be entered into R.
   > install.packages("/class/molevol-software/phybase_1.4.tar.gz",repos = NULL, type="source")
+
   > library(phybase)
  
 
== On your home machine download phybase from ==
 
== On your home machine download phybase from ==
 
     http://faculty.franklin.uga.edu/lliu/content/phybase
 
     http://faculty.franklin.uga.edu/lliu/content/phybase
 
and replace the path in the command above with your download location.
 
and replace the path in the command above with your download location.

Latest revision as of 13:48, 29 July 2017

pdf of Tutorial here

To start the lab:

Note updated links!!

log into the cluster. We will load the software we need using the command:

   module load bioware

copy the lab exercise files to your home directory

  wget https://molevol.mbl.edu/images/7/75/Edwards_species_tree_lab.zip 
  unzip Edwards_species_tree_lab.zip

for each section of the tutorial, cd in the appropriate directory.

To invoke phybase in R on the cluster:

  R

All commands after the '>' should be entered into R.

  > library(phybase)

On your home machine download phybase from

   http://faculty.franklin.uga.edu/lliu/content/phybase

and replace the path in the command above with your download location.