Install

INSTALL

• INSTALL
  • Prerequisites
  • Download the installer
  • Install
    • Debian-based OS
      • Graphical mode
      • Console mode
        • As sudo user
        • As simple user
        • Caution
        • Install
    • Fedora-based OS
      • Console mode
        • Prerequisites
          • R Install
          • RJava install
          • Python 3 install
          • Blast install
        • GEPETTO Install
  • How to use it?

Prerequisites

The [GEPETTO] installers assume you have Python3, R/RJava and Blast (from NCBI) installed. If you don't, use the following links to download and install them :

• Python3: http://www.python.org/download/
• R: http://www.r-project.org/
• RJava: http://cran.r-project.org/web/packages/rJava/index.html
• Blast :http://www.python.org/download/

The JDK 7+ (set as $JAVA_HOME) is recommended but it is embedded in the installer to be sure that you have a Java compatible version.

Download the installer

First of all, you need to download the installer. There are different versions :

• a Red Hat Enterprise Linux based compatible
• a Debian based compatible

There is 2 sort of .deb package for the Debian-based OS :

• biolo : to install in /biolo dir or in the $HOME dir
• any : to install according to the FHS (Filesystem Hierarchy Standard)

You can also find the latest snapshot release here:

Install

Debian-based OS

For GNU / Linux distributions based on Debian (Debian, Ubuntu, Mint, etc.), download the .deb file from the debian repository. Then, it is possible to easily install, either via the GUI or via the terminal.

Graphical mode

Go into the folder containing the downloaded file :

Open the deb files with GDebi by double-clicking :

Click "Install Package".

Console mode

As sudo user

Run the following command:

sudo dpkg --force-depends -i <file.deb>

or

sudo gdebi gepetto-all_version.deb --option=APT::Get::Fix-Broken=1

As simple user

If you don't have user rights, use the gepetto-all_version-biolo.deb version.

Caution

If you do not have sudo rights, you must install [GEPETTO] in a directory where you can read write and execute file : for example in your $HOME directory.

Due to the structure and standards imposed by .deb packages, this practice violates tje FHS (Filesystem Hierarchy Standard). The common procedure applied by dpkg or gdebi can not be applied. You will have to use the command dpkg -X which does not check if dependencies are satisfied on your computer. You have the responsability to check if all of those dependencies necessary for the [GEPETTO] usage are previously installed.

Install

First step to install is the copy of gepetto-all_version.deb file into the <install_dir></install_dir> that you have defined.

Go into this directory and decompress the package :

cd <install_dir> && dpkg -X <gepetto-all_version.deb> <install_dir>

Go into the [GEPETTO] directory biolo/gepetto and reconfigure the program :

cd biolo/gepetto && bash configure

Use a new terminal instance (with a shell .bashrc or .cshrc compatible) to ensure that specific commands [GEPETTO] are recognized by the console

Fedora-based OS

Console mode

Prerequisites

For Debian-based distributions (Debian, LMDE, Linux Mint, Ubuntu,...), you can
download the corresponding .deb package that will resolve and install
dependencies but for RedHat-based distributions (Red Hat Enterprise Linux, Fedora, CentOS,
Mandriva, openSUSE, SUSE Linux Enterprise,...) you have to install dependencies
manually (due to the absence of .rpm package).

R Install

sudo yum install R

RJava install

sudo R
install.packages('rJava')
quit()

Python 3 install

sudo yum install python3

Blast install

Create the /etc/yum.repos.d/rpm-sphere.repo file and put it into it (as sudo user):

[rpm-sphere]
name=RPM Sphere
baseurl=http://download.opensuse.org/repositories/home:/zhonghuaren/Fedora_17/
gpgkey=http://download.opensuse.org/repositories/home:/zhonghuaren/Fedora_17/repodata/repomd.xml.key
enabled=1
gpgcheck=1

Then install Blast using the following command :

sudo yum install ncbi-blast

After install and configure script execution (see below), please check the value of [GEPETTO ] properties into the biolo/gepetto/bin/gepetto.properties and modify the path of dependencies if its wrong.

GEPETTO Install

Choose a [GEPETTO] destination directory <installdir></installdir> and put the .tar.gz file

cd <installdir> && tar -xzvf <gepetto.tar.gz>
cd <installdir>/biolo/gepetto
sh ./configure

This will add aliases to read [GEPETTO] man pages using

mangepetto <command>

and add [GEPETTO] commands to the PATH in .bashrc and .cshrc files

To use it, you have to open a new instance of shell in the terminal (csh, tcsh, bash,...)

How to use it?

See the [Usage] page. Let's go!