Rcorrector is distributed with a version of jellyfish that seems require a complicated
set of files to run jellyfish. It turns out that all you really need is a single pre-compiled
binary for jellyfish, which we now put into $BIRCH/bin-$BIRCH_PLATFORM. Once we have
ascertained that this really works, we can delete

$BIRCH/bin-$BIRCH_PLATFORM/jellyfish.old
$BIRCH/lib-$BIRCH_PLATFORM/jellyfish.old

# Old notes for jellyfish 2.2.x
#The goal is to get a portable version of Rcorrector and the accompanying Jellyfish
#release, so that Jellyfish can also be used by other programs in BIRCH.

# Note on Makefile: Rcorrector-master/Makefile
There was a problem getting the makefile to work with the current version of
jellyfish, which is 2.2.7, so we stick with 2.2.4
Just run make on the default version of the Makefile 


#Make Symbolic links to both rcorrector and jellyfish
{venus:/home/psgendb/BIRCHDEV/bin-linux-x86_64}ln -s ../pkg/Rcorrector-master/rcorrector
{venus:/home/psgendb/BIRCHDEV/bin-linux-x86_64}ln -s ../pkg/Rcorrector-master/jellyfish/bin/jellyfish

Rcorrector-master/jellyfish/bin/jellyfish

This script by default hard-wires paths upon installation. It turns out that 
all jellyfish really needs is to have Rcorrector-master/jellyfish/bin/.libs in the LD_LIBRARY_PATH
However, for portability we have a separate lib directory for each platform, and
use the BIRCH_PLATFORM directory to find it. The jellyfish script has been modified to
that end. 

To add a new platform, all that should be necessary is to remake jellyfish on the new
platform and add a jellyfish directory to the lib-$BIRCH_PLATFORM directory for that
platform.