Notes on running the GeneFamilyPipe (GFP) programs
June, 2003   Steven Cannon   cann0010@umn.edu

Note: These are the scripts that I use in my day-to-day research. Primarily, 
these scripts control lots of other bioinformatics programs, and manage format 
conversions and some data clean-up associated with phylogenetic tree 
construction. The nature of the process is that it requires the installation 
of a lot of other software. Much of this is standard stuff in bioinformatics, 
but it does require quite a bit of work to install. I have made some 
installation instructions at 
http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html
However, due to time constraints, I have to say "you're on your own" in doing 
the installations. That said, I would like to hear bug reports about the 
pipeline programs.

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The scripts in this pipeline all take parameters from config files. In the
current distribution, there is a set of config files for Arabidopsis data. 

The scripts, config files, and sample files are each located in their own 
directories in the distribution. 

GeneFamilyPipe
  scripts       scripts
  cfg           config files for the Arabidopsis example
  Athal         data for the Arabidopsis example

The config files are currently set up to be called from the scripts directory. 
No installation or modification of your PATH is required. For example, cd into 
the scripts directory and call a program and its config file in this way:
  10_GetFastaSubset ../cfgAthal/10.cfg

The scripts can be placed in your PATH and called from another location, but the 
config files will need to be changed accordingly.

Using the full set of scripts requires installation these programs:
  BioPerl
  NCBI Blast
  Clustalw
  T-Coffee
  Tree-Puzzle
  hmmer
  
  (Next: for the ExpressTreePipeline scripts, not included in main distro)
  lwp
  LWP::Simple