2. TGFam-Finder installation > Manual

Prior to installation of TGFam-Finder, users should complete installation of following programs, Perl 5.6.1 or higher version, Bioperl, and YAML (perl module). Then, an auto-installation script in TGFam-Finder performs installation of the other prerequisite tools, including Bowtie2-2.3.1, HMMER-3.1b2, BLAST 2.6.0+, InterproScan-5.22-61.0, Exonerate-2.2.0, Blat v35, Tophat-2.1.1 and Cufflinks-2.2.1, Augustus-3.2.3, Scipio-1.4, and ClustalW-2.1, with yum (apt-get) update to perform annotation using TGFam-Finder. If users already updated yum (apt-get), the auto-installation process can be performed using general user account as well as root authority.

2.1 System requirements for installation of TGFam-Finder

- Hard drive capacity: over 20 Gb storage

- OS: Fedora CentOS version 6 or higher (Ubuntu version 16.04 or higher)

- Prerequisite softwares: 1) Perl 5.6.1 or higher version, Bioperl, and YAML (perl module), 2) Yum (Ubuntu: apt-get), and 3) Bowtie2-2.3.1, HMMER-3.1b2, BLAST 2.6.0+, InterproScan-5.22-61.0, Exonerate-2.2.0, Blat v35, Tophat-2.1.1 and Cufflinks-2.2.1, Augustus-3.2.3, Scipio-1.4, and ClustalW-2.1

- Prerequisite softwares in the first category should be installed before installation of the tools in the second and the third categories. TGFam-Finder provides a script that allows automatic installation of tools in the second and the third categories. If users cannot access root account, Yum (or apt-get) should be installed or updated as the latest version before the auto-installation process. Then, users can perform the auto-installation using any account.
 

2.2 Download TGFam-Finder script

- You can download TGFam-Finder script in TGFam-Finder web site (http://tgfam-finder.snu.ac.kr) or Github (https://github.com/tgfam-finder).
 

Usage:

- CentOS (Fedora, Redhat series)

$wget http://tgfam-finder.snu.ac.kr/download/TGFam-Finder_CentOS_v1.01.tar.gz 

or $git clone https://github.com/tgfam-finder/scripts_centos.git

- Ubuntu Series (Debian series)

$wget http://tgfam-finder.snu.ac.kr/download/TGFam-Finder_Ubuntu_v1.01.tar.gz

or $git clone https://github.com/tgfam-finder/scripts_ubuntu.git
 

2.3 Extraction of the downloaded file

Usage:
$tar zxvf file_name,
ex) tar zxvf TGFam-Finder_CentOS_v1.01.tar.gz

2.4 Installation

Basically, the installation script performs full auto-installation of the prerequisite tools that we mentioned in the section “System requirements for installation of TGFam-Finder”. Considering huge size of InterproScan causing download delay, users can do partial installation except for installation of InterproScan v5. We recommend that if users are hard to download InterproScan through our package, users should use the install script (option "N") after direct download from the website (https://www.ebi.ac.uk/interpro/download.html) and self-installation of InterproScan. For users who want to manually setup the prerequisite tools, users can only use the annotation scripts. If users consider manual installation of all prerequisite tools, see the section 5 “Information of the used prerequisite tools”

Usage:
$perl install_TGFam-Finder.pl absolute_installation_path

(ex. $perl install_TGFam-Finder.pl /home/TGFam-Finder/TGFam)

  

If you want to confirm completion of installation, you need to check list of programs that installed in the installation path.