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Copy file name to clipboardExpand all lines: doc/source/Tutorials_Tutorial21.rst
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Import human KEGG pathway modules using Gitools
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- Import human KEGG pathways. See `this chapter <UserGuide_KEGG.rst>`__ of the user guide for further guidance.
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- Import human KEGG pathways. See :doc:`this chapter <UserGuide_KEGG>` of the user guide for further guidance.
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- Select “Affy HG U133-PLUS-2” as identifiers for the genes, which correspond to the probe identifiers we have in our dataset.
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Perform an enrichment analysis with Gitools
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-------------------------------------------
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- See `this chapter <UserGuide_Enrichment.rst>`__ for details on how to perform enrichment analysis
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- See :doc:`this chapter <UserGuide_Enrichment>` for details on how to perform enrichment analysis
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- Select gse19188\_median-centered.cdm.gz as data file
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- Give a name to the analysis. Select a directory where to safe it and click Finish.
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- If you have a memory problem, see memory configuration in ( `Installation Guide <UserGuide_Installation.rst>`__ ) to increase the memory allocated to run Gitools.
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- If you have a memory problem, see memory configuration in ( `Installation Guide <UserGuide_Installation>` ) to increase the memory allocated to run Gitools.
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Use annotations for pathways and annotation colors for samples
Copy file name to clipboardExpand all lines: doc/source/UserGuide_Installation.rst
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.. contents::
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Installing Gitools locally
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-----------------------------
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Extract and execute
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---------------------
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You can download the last version of Gitools from `http://www.gitools.org/download <http://www.gitools.org/download>`__
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Gitools depends on Java 7 or higher. Java must be installed in order to run Gitools. Once Java is set up, follow
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Gitools depends on Java 7 (also called 1.7) or higher. Java must be installed in order to run Gitools. Once Java is set up, follow
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the steps below.
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* Download the latest Gitools version
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* Uncompress the zip file into a folder (preferably in your Applications folder)
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* Enter the Gitools-folder called where you find another folder called, ``bin``. *Depending on your operating system* you will have to click or double click one of the following files:
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* Windows: **gitools-2GB.bat**
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* Enter the Gitools-folder. *Depending on your operating system* you will have to click or double click one of the following files:
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* Windows: **gitools.exe**
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* Mac OS X: **gitools**
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* Linux: **gitools**
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Setting up Java JDK
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Windows
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--------------------------------------
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If your system doesn not have Java already installed, dwonload the latest version of
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**Java 7 JDK**, from `www.oracle.com/technetwork/java/javase/downloads <www.oracle.com/technetwork/java/javase/downloads>`__.
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Depending on your platform download the file for:
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* Linux x64
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* Mac OS X x64
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* Windows x64
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Specific instructions for Windows
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If your machine is not a 64-bit machine, download the x86 version
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Java JDK installation
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##########################
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Depending on the platform the installation is different:
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If Java is not yet installed download the **Java 7 JDK** from `http://www.oracle.com/technetwork/java/javase/downloads <http://www.oracle.com/technetwork/java/javase/downloads>`__.
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**Windows**
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* If your machine is not a 64-bit machine, download the x86 version.
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* Install the .exe file
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Install the .exe file
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Memory configuration
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########################
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**OS X**
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The windows executable (gitools.exe) tries to find out how much RAM is available and assigns it to the application.
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If you get an error that says *java.lang.OutOfMemoryException*, please free some RAM before running Gitools
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Install the .dmg file normally. Note that you need to install the JDK version of Java, otherwise Gitools
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does not have access to the updated java.
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Adding Gitools to the command line (optional)
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###############################################
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**Linux**
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- You need to have java installed. Go to this website to download and install; `http://www.java.com/en/download/You <http://www.java.com/en/download/You>`__
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- `http://www.java.com/en/download/You <http://www.java.com/en/download/You>`__ need to add path of java after set up; go here to do this: `http://www.java.com/en/download/help/path.xml. <http://www.java.com/en/download/help/path.xml.>`__ This will tell your computer where to find the java program add these two paths: **c:\\ java-directory\\ bin** and **c:\\ java-directory\\ lib** where c:\\ javadirectory will be the place where java is installed and where the bin and lib directors are found in the java installation directory.
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- You need to add the path of the Gitools bin directory also in order to run the Gitools in the same path variable ( just like you added the other two paths) add ** c:\\ gitoolsdirectory\\ bin** and **c:\\ gitoolsdirectory\\ lib** to the path variable. All path variables must be added to existing path (be careful not to delete anything which is already there) and separate each new path with a semicolon. The new path can be added to the front of the existing path followed by a semicolon to separte other existing entries.
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- To run the Gitools; just click on the gitools.bat file. You can make a shortcut for this file by righclick and say send to ‘desktop’ and it will creat a shortcut on your desktop for future use.
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* Extract the download Java file into a folder
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* Open the file ``~/.bashrc`` in order to edit system variables:
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* Export the ``JAVA_HOME`` java installation folder as follows: ``export JAVA_HOME="/path/to/folder/jdk1.7.0_60``
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* Add the bin filder to your path as follows: ``export PATH = $JAVA_HOME/bin:$PATH``
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* Save the file and start gitools from a new terminal
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Memory configuration
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-----------------------
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OS X
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--------------------------------------
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Gitools is a Java application, and by default it starts with the default memory requirements stablished by most of the Java applications (usually 256 Megabytes). But most probably you will need more than the default, you will realize this when you obtain an exception like this:
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Specific instructions for OS X
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*java.lang.OutOfMemoryException*
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Java JDK installation
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##########################
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There is a way to configure the memory limits for Gitools the same way that Java does, using the option *-Xmx*. But this configuration should be specified through an enviroment variable called **GITOOLS\_JAVA\_OPTS**. Let’s see some examples of how to do this with different operating systems:
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If Java is not yet installed download the **Java 7 JDK** from `http://www.oracle.com/technetwork/java/javase/downloads <http://www.oracle.com/technetwork/java/javase/downloads>`__.
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**Windows**
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Install the .dmg file normally. Note that you need to install the JDK version of Java, otherwise Gitools
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does not have access to the updated java.
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- Right-click the **My Computer** icon on
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- your desktop and select **Properties**.
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- Click the Advanced tab. Click the
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- Environment Variables button. Under System Variables, click New.
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- Enter the variable name as **GITOOLS\_JAVA\_OPTS**.
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- Enter the variable value as follows for 2 GB: **-Xmx2g**.
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- Click OK.
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- Click Apply Changes.
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Memory configuration
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########################
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**Linux**
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Imagine that you want to use 1024 megabytes of memory for Gitools, then edit the **~/.bashrc** file adding a line like this:
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Imagine that you want to use 1024 megabytes of memory for Gitools, then edit the **bin/gitools.vmoptions** and **bin/gitools64.vmoptions**
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changing the first line accordingly:
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``export GITOOLS\_JAVA\_OPTS = ’-Xmx1024m’``
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``-Xmx1024m``
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You can also specify 2 gigabytes like this:
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``export GITOOLS\_JAVA\_OPTS = ’-Xmx2g’``
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``-Xmx2g``
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**Mac OS X**
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Adding Gitools to the command line (optional)
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###############################################
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Imagine that you want to use 1024 megabytes of memory for Gitools, then edit the **~/.profile** file adding a line like this:
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``export GITOOLS\_JAVA\_OPTS =”-Xmx1024m”``
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Imagine that you have uncompressed the zip file into */opt/gitools-2.2.0-bin*. In this case you can add
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Gitools to the command line changing the *PATH* variable. In order to do this, just open **~/.profile** file and add
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this line at the bottom :
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You can also specify 2 gigabytes like this:
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``export PATH=/opt/gitools-2.2.0-bin:$PATH``
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``export GITOOLS\_JAVA\_OPTS =”-Xmx2g”``
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Start a new terminal and you should be able to run Gitools graphical interface typing:
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``gitools``
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Java Web Start
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--------------
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Java Web Start is a technology that allows running Java applications directly from the web. This method is very convenient to evaluate the tool, but when used for daily work and to use big amounts of data is better to install it locally.
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In the `main page of Gitools <http://www.gitools.org>`__ there is an orange button that says *Launch*. Simply click on it and the application will be downloaded and executed automatically.
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It is very easy to use but sometimes the internet navigator doesn’t know how to communicate with Java and launch the application. You can use the following terminal command to launch it:
If Java is not yet installed download the **Java 7 JDK** from `http://www.oracle.com/technetwork/java/javase/downloads <http://www.oracle.com/technetwork/java/javase/downloads>`__.
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Adding Gitools to the command line (Advanced)
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-----------------------------------------------
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* If your machine is not a 64-bit machine, download the x86 version.
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* Extract the download Java file into a folder
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* Open the file ``~/.bashrc`` in order to edit system variables:
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* Export the ``JAVA_HOME`` java installation folder as follows: ``export JAVA_HOME="/path/to/folder/jdk1.7.0_60``
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* Add the bin filder to your path as follows: ``export PATH = $JAVA_HOME/bin:$PATH``
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* Save the file and start gitools from a new terminal
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**Mac OS X**
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Memory configuration
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########################
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Imagine that you have uncompressed the zip file into */opt/gitools-1.5.0-bin*, then you can define the *PATH* variable in
Imagine that you want to use 1024 megabytes of memory for Gitools, then edit the **bin/gitools.vmoptions** and **bin/gitools64.vmoptions**
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changing the first line accordingly:
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Start a new terminal and you should be able to run Gitools graphical interface typing:
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``-Xmx1024m``
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``gitools``
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You can also specify 2 gigabytes like this:
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``-Xmx2g``
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**Linux**
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Adding Gitools to the command line (optional)
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###############################################
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Imagine that you have uncompressed the zip file into * /opt/gitools-1.5.0-bin*, then you can define the *PATH* variable
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in the **~/.bashrc** file adding a line like this:
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Imagine that you have uncompressed the zip file into */opt/gitools-2.2.0-bin*. In this case you can add
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Gitools to the command line changing the *PATH* variable. In order to do this, just open **~/.bashrc** file and add
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this line at the bottom :
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``export PATH=/opt/gitools-1.5.0-bin/bin: $PATH``
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``export PATH=/opt/gitools-2.2.0-bin:$PATH``
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Start a new terminal and you should be able to run Gitools graphical interface typing:
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``gitools``
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**Windows**
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Java Web Start
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--------------
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Java Web Start is a technology that allows running Java applications directly from the web. This method is very convenient to evaluate the tool, but when used for daily work and to use big amounts of data is better to install it locally.
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- You need to have java installed. Go to this website to download and install; `http://www.java.com/en/download/You <http://www.java.com/en/download/You>`__
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- `http://www.java.com/en/download/You <http://www.java.com/en/download/You>`__ need to add path of java after set up; go here to do this: `http://www.java.com/en/download/help/path.xml. <http://www.java.com/en/download/help/path.xml.>`__ This will tell your computer where to find the java program add these two paths: **c:\\ java-directory\\ bin** and **c:\\ java-directory\\ lib** where c:\\ javadirectory will be the place where java is installed and where the bin and lib directors are found in the java installation directory.
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- You need to add the path of the Gitools bin directory also in order to run the Gitools in the same path variable ( just like you added the other two paths) add ** c:\\ gitoolsdirectory\\ bin** and **c:\\ gitoolsdirectory\\ lib** to the path variable. All path variables must be added to existing path (be careful not to delete anything which is already there) and separate each new path with a semicolon. The new path can be added to the front of the existing path followed by a semicolon to separte other existing entries.
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- To run the Gitools; just click on the gitools.bat file. You can make a shortcut for this file by righclick and say send to ‘desktop’ and it will creat a shortcut on your desktop for future use.
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In the `main page of Gitools <http://www.gitools.org>`__ there is an orange button that says *Launch*. Simply click on it and the application will be downloaded and executed automatically.
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It is very easy to use but sometimes the internet navigator doesn’t know how to communicate with Java and launch the application. You can use the following terminal command to launch it:
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