User:DukeEgr93/SNIPR

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  • 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, Bioinformatics, Robust Control. 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
From MATLAB's help site
  • 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

Round Two

Fedora

Made a Virtualbox with Fedora, downloaded ISO, connected to optical first time around, disconnected from optical second time around, etc

cmake

  • Opened terminal
  • sudo dnf install cmake
  • sudo yum install gcc-c++

NUPACK

  • NUPACK
    • Registered
    • Downloaded and moved to home directory
    • gunzip nupack3.2.2.tar.gz
    • tar -xvf nupack3.2.2.tar
    • cd nupack3.2.2
    • mkdir build
    • cd build
    • sudo cmake ../
    • sudo make
    • Fail...