0.Quick Start

To use the Octopus-toolkit right away, please follow these tutorials:

0-1. Installation Movie Clip

Tutorial for installation. (Youtube)

0-2. Ubuntu(16.04), Mint(18) (We highly recommend to use Ubuntu)

• Commands (Quick_Start(Ubuntu,mint).txt):

  sudo apt-get update
  sudo apt-get install openjdk-8-jdk
  sudo apt-get install zlib1g-dev libpng12-dev libncurses5-dev build-essential r-base
  wget http://octopus-toolkit2.readthedocs.io/en/latest/_downloads/Octopus-toolkit.zip -O Octopus-toolkit.zip
  unzip Octopus-toolkit.zip
  cd Octopus-toolkit/
  java -jar Octopus-toolkit.jar
  

0-3. Fedora(25)

• Commands (Quick_Start(Fedora).txt):

  sudo yum update
  sudo yum install java-1.8.0-openjdk
  sudo yum install zlib-devel.x86_64 libpng-devel.x86_64 libpng12-devel.x86_64 ncurses-devel.x86_64 gcc-c++ bzip2-devel xz-devel R
  wget http://octopus-toolkit2.readthedocs.io/en/latest/_downloads/Octopus-toolkit.zip -O Octopus-toolkit.zip
  unzip Octopus-toolkit.zip
  cd Octopus-toolkit/
  java -jar Octopus-toolkit.jar
  

0-4. CentOS(7)

• Commands (Quick_Start(CentOS).txt):

  sudo yum update
  sudo yum install java-1.8.0-openjdk
  sudo yum install zlib-devel.x86_64 libpng-devel.x86_64 libpng12-devel.x86_64 ncurses-devel.x86_64 gcc-c++ bzip2-devel xz-devel
  sudo yum install epel-release
  sudo yum install R
  wget http://octopus-toolkit2.readthedocs.io/en/latest/_downloads/Octopus-toolkit.zip -O Octopus-toolkit.zip
  unzip Octopus-toolkit.zip
  cd Octopus-toolkit/
  java -jar Octopus-toolkit.jar
  

0-5. MacOS(Sierra 10.12.6)

Note

Please refer to the link below for MacOS

Link : 1.Installation 1-6.MacOS(Sierra_10.12.6)

0-6. Quick Run (Public data)

Example GSE file (Example_GSE_List.txt)

• A : Click the OPEN button.
• B : Select the Example_GSE_List.txt file.

• C : Click the RUN button.
• D : Set parameters. Then, click the RUN button.

• Octopus-toolkit will sequentialy download and process the data specified in the list file. The analysis may take some time.

• Below shows output file of Octopus-toolkit