Installation

Quick Start

1. Verify that you have installed the basic dependencies.
2. To use the 1D-Function that provides reference genome indexing, alignment of fastq files and filtering of alignment files, follow the instructions here for the dependencies download and installation. NOTE: This step is required only for the 1D-Functions tools.
3. Download the latest GenomeFlow Tools jar
4. Run GenomeFlow:
   • Windows OS: double-click the genomeflow.bat script
   • Linux/UNIX based OS: execute the script, genomeflow.sh

Basic dependencies

Java 1.7 or 1.8 JDK. (Alternative link for Ubuntu/LinuxMint). Minimum system requirements for running Java can be found at http://java.com/en/download/help/sysreq.xml .
These dependencies support only the 2D-Functions and 3D-Functions Tools.

1D-Functions Dependencies

Operating System (OS)

A Linux, UNIX, or Mac OS X environment is required to use the 1D-Functions.

It is strongly recommended to work under a Mac OS X or a Linux/UNIX-based operating system, such as Ubuntu, Centos/Red Hat, Solaris.

If you are using a Windows operating system, install Cygwin first. Cygwin is a free software that provides a UNIX-like environment on Windows. The Cygwin install package can be found here. Once Cygwin is installed, place your work in the Cygwin directory.

Download External Tools

• Download Bowtie2 OR BWA for indexing and alignment creation.
• Bowtie2 supports multiple OS, download the version for your OS. That is:
  • Download bowtie2- version number-macos-x86_64 for MacOS
  • Download bowtie2- version number- linux-x86_64 for Linux
  • Download bowtie2- version number- mingw-x86_64 for Mingw/Cygwin
• Download Samtools (http://samtools.sourceforge.net/)
• We tested on the following versions for each one of the tools: bowtie2-2.3.4-*, bwa-0.7.17, and samtools-1.6.
• You can also download the installation files for these tools from here

Installing External Tools

Bowtie2

• Open a Unix Terminal
• Change directory to the downloaded Bowtie2-* directory. For example:
  • cd bowtie2-2.3.4-linux-x86_64
• Give executable permission to the binary file. For example:
  • In Unix based Operating system/ Cygwin/Mingw: chmod +x bowtie2*

BWA

• Open a Unix Terminal
• Change directory to the downloaded bwa-* directory. For example:
  • cd bwa-0.7.17
• Type make once you are inside the bwa directory. For example:
  • make
• This operation produces a binary file: bwa
  • In Unix based Operating system: bwa
  • In Cygwin/Mingw: bwa.exe
• Give executable permission to the binary file. For example:
  • In Unix based Operating system: chmod +x bwa
  • In Cygwin/Mingw: chmod +x bwa.exe

Samtools

• Open a Unix Terminal
• Change directory to the downloaded samtools-* directory. For example:
  • cd samtools-1.7
• Type ./configure once you are inside the samtools directory. For example:
  • ./configure
• After configuration is completed, type make. For example:
  • make
• This operation produces a binary file: samtools
  • In Unix based Operating system: samtools
  • In Cygwin/Mingw: samtools.exe
• Give executable permission to the binary file. For example:
  • In Unix based Operating system: chmod +x samtools
  • In Cygwin/Mingw: chmod +x samtools.exe

Gawk

• Open a Unix Terminal
• Install gawk
• For Linux Users
  • Type sudo apt-get install gawk
• For Mac OSX Users:
  • Follow the instructions here: http://macappstore.org/gawk/
• For Cygwin/Mingw Users:
  • Open a Unix terminal
  • Download gawk-4.2.1.tar.gz
    • wget https://ftp.gnu.org/gnu/gawk/gawk-4.2.1.tar.gz
  • Unzip the gawk-4.2.1.tar.gz
    • tar -xvpzf gawk-4.2.1.tar.gz
  • Change directory to the gawk-4.2.1 directory
    • cd gawk-4.2.1
  • Type ./configure once you are inside the gawk-4.2.1 directory.
    • ./configure
  • After configuration is completed, type make. For example:
    • make && make check