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Brief introduction to unix
1.command line driven
	type commands into the terminal and press <enter>
	commands and file names are case sensitive
	do not use spaces in your filenames!!!
2. folders are called directories
	to list contents of directories type “ls”
	to change directories type “cd” followed by directory name
	to make a new directory type “mkdir”
3. deleting, renaming, moving and copying files
	renaming and moving files use the same command: 
	mv oldname newname
	mv oldlocation newlocation
		deleting is forever!
	rm filename
		unix will not ask you if you are sure.
	copying: cp oldname newname
	
4. shortcuts for lazy typists:
	up arrow will show you the previous command.  repeating the up arrow will cycle through previous commands
	history shows you all prior commands stored - helpful if you don't remember syntax of complicated command
		!108 will execute the 108th command
^E takes you to end of line
^A takes you to beginning of line
	tab completion: once you type the beginning of a filename, if you type "tab" and the name is unique, unix will fill in the rest of the filename.
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back to software installation: GENESIS
	
1. install one more library.  Become superuser:
"su"
then enter the first password you gave when installing the software

then type "yum install flex-static.x86_64
say yes whenever it asks.

2. Download genesis from www.genesis-sim.org/GENESIS/genesis-ftp
Get genesis-2.3-src.tar.gz (from www.genesis-sim.org/GENESIS you can also download various tutorials and view the hypertext manual.)
From your main directory, type:
"mv Downloads/genesis-2.3-src.tar.gz .."
then tar -xzf genesis-2.3-src.tar.gz
cd genesis-2.3/genesis/src

3. Edit the Makefile as follows:
copy the Makefile.dist to Makefile: cp Makefile.dist Makefile
edit the Makefile:
gedit Makefile

scroll down to the part that says
# System:	Linux 1.2.x and up on Intel x86-based, Xeon,
remove comments (#) from the following lines:
MACHINE=Linux
OS=BSD

XINCLUDE=-I/usr/X11R6/include

XLIB=/usr/X11R6/lib64

CC=cc
CPP=cpp -P
CFLAGS=-O2 -D__NO_MATH_INLINES -DLONGWORDS

LD=ld
RANLIB=ranlib
AR=ar

YACC=bison -y
LEX=flex -l
LEXLIB=-lfl
LIBS= $(LEXLIB) -lm

TERMCAP=-lncurses
TERMOPT=-DTERMIO -DDONT_USE_SIGIO

save the file, and exit
4. compile the software
you can either type "make" or "make >& make.out"
if you type make, just look at the last few lines when it's done.  If you type make >& make.out, then when it is done, type
"tail make.out"
at the end of this file it should say "Full GENESIS Compiled -- All Done

5. then type:
make install

at the end you should see "Done with full install"

6. copy file .simrc into your home directory:
cd ..
now you should be in the genesis-2.3/genesis directory
cp .simrc ../../
This puts the file in your own home directory, needed for proper running of the file.  

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It is annoying to always specificy the location (known as full path) of the file you want to run.  One way to avoid this is to tell the  computer to look in the xpp directory and/or the genesis directory.  
We do this by editing the file .bashrc (in your home directory)
gedit .bash_profile

edit the following line:

	PATH=$PATH:$HOME/.local/bin:$HOME/bin

	so that it says
	PATH=$PATH:$HOME/.local/bin:$HOME/bin:$HOME/genesis-2.3/genesis:$HOME/genesis2.3/chemesis2.1:$HOME/xppaut
	
	then save it and exit.
	
type
	.source bash_profile
	
	this will make the computer look in those directories, so now when you type xppaut, no matter what directory you are in, the computer will find xppaut.
	
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Now, to install chemesis.
1. Download chemesis from my website : http://krasnow1.gmu.edu/CENlab/software.html
2. put chemesis into the top level genesis directory:
cp Download/chemesis2.1.tar.gz genesis-2.3

3. find out what is the name of your directory by typing "pwd"
this will return something like "/home/avrama" - you need this for the INSTALLDIR below

cd genesis-2.3
tar -xzf chemesis2.1.tar.gz
cd chemesis2.1
cp Makefile2.3 Makefile

Edit the makefile:
gedit Makefile

edit the line that begins INSTALLDIR   = 
INSTALLDIR   =  /home/avrama/genesis2.3/genesis
and the line that begins CFLAGS = 
CFLAGS	  = -O2 -D__NO_MATH_INLINES -DLONGWORDS

exit, and then type:
cd chan
cp Makefile2.3 Makefile
cd ..
then
type Make

and that should work.

test it by typing 
./chemesis
listobjects
and look for something called "rhodopsin"
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short introduction to genesis: http://www.genesis-sim.org/GENESIS/Tutorials/genprog/tut1-lite.html
Getting started - 
	Moving about in genesis
	Creating elements
	examining elements
	Modifying elements
	adding graphics
	linking elements
http://www.genesis-sim.org/GENESIS/Tutorials/genprog/tutorial1.html 
skip adding buttons