User:DukeEgr93/SNIPR

• Installed VirtualBox 6.1.18 from [1] using all defaults
• Created a machine in VirtualBox Manager using New; 4 GB Ram; 100 GB VDI drive fixed size for speed
• Downloaded Ubuntu from Ubuntu and installed it
  • After installation, stop the machine and remove the optical ISO if need be
• Used Firefox to connect to MATLAB and installed R2017a with "sudo ./install" to have access to folders; MATLAB, Simulink, and Bioinformatics Toolbox required. To be able to add toolboxes later, in UNIX:

sudo apt-get install libgconf-2-4
cd /usr/local.MATLAB/R2017a/bin/glnxa64
sudo mkdir exclude
sudo mv libfreetype.so.6 exclude

• NUPACK
  • Registered
  • Downloaded and opened with archive manager
  • Extracted to /home/ID
  • Installed cmake with

sudo apt install cmake

• Installed g++ with

sudo apt install g++

• Change to nupack folder, make build, change to build,

sudo cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ ../
sudo make
sudo make install

Sooooo many warnings...

• Install most recent version of libstdc++

sudo apt install compat-libstdc++-33.x86_64

• Find most recent version of libstdc++

locate libstdc++

If locate does not work, use

sudo apt install mlocate 

first. Find the one that is in /usr/lib/x86_64-linux-gnu

• Add lines to bash profile and run it:

 pico ~/.bash_profile

and add

export NUPACKHOME=/home/mrg/nupack3.2.2
export PATH=$PATH":${NUPACKHOME}/bin"
export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28"

then

source ~/.bash_profile

Not sure if required since these live on /usr/local

• Start MATLAB from terminal

cd /usr/local/MATLAB/R2017a/bin
./matlab &

• Check to see if things are working

system('musltitubedesign')

• SNIPR
  • Change into home

cd 

• Get github repository

sudo apt install git
git clone https://github.com/Albert09111/SPIPR/

• Change into SNIPR Folder

cd SNIPR

• Run MATLAB

/usr/local/MATLAB/R2017a/bin/matlab &

• In MATLAB, run SNIPR

SNIPR