Re: [AMBER] Question about AmberTools14/15 installation

From: Novosielski, Ryan <novosirj.ca.rutgers.edu> Date: Mon, 8 Feb 2016 10:41:10 -0500

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________________________________________
From: A kS [aks25121986.gmail.com]
Sent: Monday, February 08, 2016 3:15 AM
To: AMBER Mailing List
Subject: [AMBER] Question about AmberTools14/15 installation
Dear AMBER user,
I am new to AMBER. I am trying to install the AmberTools14 and AmberTools15
in Ubuntu 12.04 64 bit system. After reading the Jason Swails installation
instruction and doing some trials with both the AmberTools I found that the
amber.sh file have these lines :
*********************************************************************************************************in
AmberTools14:*
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
   export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${AMBERHOME}/lib"
fi
*in AmberTools15*:
if [ -z "$PYTHONPATH" ]; then
    export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
else
    export
PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
   export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
fi
*******************************************************************************************************************
*Instruction says that after doing ./configure we can do "source amber.sh"
and after make install "echo "source $AMBERHOME/amber.sh" >> ~/.bashrc"*
My problems are:
1.  I am unable to clearly understand the meaning of that "if else loop".
What I found out that, if [ -z "something" ] means: if "something" is
absent then do task1 else task2. So when I source that amber.sh in terminal
how exactly it add all paths to my .bashrc file, at least the syntax.
2. Doing "*echo "source $AMBERHOME/amber.sh" >> ~/.bashrc*" will add the
"source $AMBERHOME/amber.sh" line  to .bashrc and how it will help to run
AMBER in future.
3. I learned little bit of old style of adding path to .bashrc. So I add
these lines to .bashrc for all the AmberTools
*********************************************************************************
export AMBERHOME=/home/a/application/ambertools15
#export AMBERHOME=/home/a/application/ambertools14
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
export PATH=$AMBERHOME/bin:$PATH
export DO_PARALLEL='mpiexec.hydra -n 8'
**************************************************************************************
so that whenever I need any of the amberttools (i know its silly cause now
AmberTools15 have all the features of its previous version) I just comment
the other AMBERHOME containing line.
Is it correct one??
I know these are silly questions but without solving them I am unable to
move forward. So any suggestion will be immense helpful for me.
Regards
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