User:DukeEgr93/SNIPR

Ubuntu on a VirtualBox

Virtual Machine

• Created a machine in VirtualBox Manager using New; 8 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
• Need to install:

sudo apt-get install gcc
sudo apt-get install g++
sudo apt-get install cmake
sudo apt-get install mlocate 
sudo apt-get install git

• Also need to be using gcc-9; if 10 is installed:

sudo apt install gcc-9 g++-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 100 --slave /usr/bin/g++ g++ /usr/bin/g++-9 --slave /usr/bin/gcov gcov /usr/bin/gcov-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 90 --slave /usr/bin/g++ g++ /usr/bin/g++-10 --slave /usr/bin/gcov gcov /usr/bin/gcov-10

MATLAB

• Used Firefox to connect to MATLAB, downloaded and saved to Downloads
• Extract and install:

cd ~/.Downloads
unzip matlab_R2017b_glnxa64.zip
sudo ./install

• Need to have MATLAB, Simulink, Bioinformatics, Robust Control, Statistics and Machine Learning, and Control System Toolbox.
  • Note: If you didn't install the right toolboxes, to be able to add toolboxes later, in UNIX:

sudo apt-get install libgconf-2-4
cd /usr/local/MATLAB/R2017b/bin/glnxa64
sudo mkdir exclude
sudo mv libfreetype.so.6 exclude

From MATLAB's help site

• Move libstdc++.so so it does not interfere with the new one

cd /usr/local/MATLAB/R2017b/sys/os/glnxa64
sudo mv libstdc++.so.6 libstdc++.so.6.OLD

NUPACK

• NUPACK
  • Registered
  • Downloaded and saved to Downloads

cd ~/Downloads
gunzip nupack3.2.2.tar.gz
tar -xvf nupack3.2.2.tar
cd nupack3.2.2
mkdir build
cd build
sudo cmake ../
sudo make
sudo make install

Sooooo many warnings with make

Prepare Shell

• Edit ~/.bash_profile and add lines; use

pico ~/.bash_profile

in the terminal, add the lines:

export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
alias matlab='/usr/local/MATLAB/R2017b/bin/matlab'

then save and exit

• First time you do this, in the terminal type

source ~/.bash_profile

Check MATLAB

• Run MATLAB

matlab

• Try to run multitubedesign

system('multitubedesign')

SNIPR

• Change into home

cd 

• Get github repository

git clone https://github.com/Albert09111/SNIPR/

• Change into SNIPR Folder

cd SNIPR

• Run MATLAB (assumes alias is working)

matlab &

• In MATLAB, run SNIPR

SNIPR