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## xTract installation
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The xTract pipeline has been developed in Perl (version 5.10.0). It was developed and tested on Linux based operating systems.
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### 1. General
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This section describes the installation on a Unix based system (Ubuntu). For installation on a single machine, we recommend to use Ubuntu as OS. For fast processing we recommend to use a computer/server with sufficient (e.g. 48GB) RAM.
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### 2. Installation of Prerequisites and xTract
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#### 2.1. Installation of Perl packages
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The program relies on some Perl packages that do not come with the standard Perl installation. The required Perl packages are:
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```
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* BioPerl
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* Data::Dumper
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* File::Copy
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* MIME::Base64
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* HTML::TreeBuilder
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* XML::TreeBuilder
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* Math::Gauss
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* Math::Trig
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* Statistics::Regression
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* Statistics::TTest
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* Chart::Gnuplot
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* Statistics::Distributions
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* Term::ReadKey
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* Time::HiRes
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```
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Install these perl packages on your system (e.g. by using cpan).
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`>sudo cpan Data::Dumper`
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#### 2.2. Installation of fromdos tool
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Intall the tool "fromdos".
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`>sudo apt-get install tofrodos`
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#### 2.3. Installation of R
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Intall R, a programming language for statistical computing.
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`>sudo apt-get install r-base`
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#### 2.4. Installation of xTract
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1. Download the source tar archive from the Download section and save it on your computer (e.g. /home/user/V1_0_0.tar).
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2. Create an installation directory. e.g. /home/user/xtract
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`>mkdir xtract`
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3. Extract the tar archive to the installation directory.
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`>tar -xvf V1_0_0.tar -C xtract`
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This command will extract the program to /home/user/xtract/V1_0_0/...
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4. Convert the scripts in the /bin directory to the UNIX format.
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`>fromdos -v xtract/V1_0_0/bin/*`
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5. Add the /bin folder to your PATH variable.
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For example, edit and add the following line to your .bashrc file.
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`export PATH="/home/user/xtract/V1_0_0/bin:$PATH";`
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#### 2.5. Installation of IPC
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IPC (Isotopic Pattern Calculator) is used to calculate the isotope abundances of a given peptide.
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IPC can be downloaded from: [http://isotopatcalc.sourceforge.net/](http://isotopatcalc.sourceforge.net/) or you can find a copy of IPC (version 1.4) in the xTract installation folder: /home/user/xtract/V1_0_0/ipc/ipc-1.4.tar.gz
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```
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cd /home/user/xtract/V1_0_0/ipc/
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tar xfz ipc-1.4.tar.gz
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cd ipc-1.4
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./configure
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make all
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sudo make install
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```
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This will install IPC to /usr/local/bin/ipc which will be already available in your PATH. If you install IPC to another directory use ./configure prefix=/home/.../ and add the directory to your PATH. IPC should now be availaible as the command `>ipc` on your terminal.
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#### 2.6. Gnuplot
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Gnuplot is used for plotting (optional) and should be available on most Unix distributions. Check if you have gnuplot installed by typing `>gnuplot` on your terminal.
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### 3. Define paths for ipc and gnuplot
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This is only relvant if ipc and/or gnuplot are not available in your PATH. In this case you can define the paths of the programs in a configuration file. Open the file /home/user/xtract/V1_0_0/conf/xTract_environment_config and edit the paths as indicated.
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Now you can use xTract as described in How to run. |
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