Difference between revisions of "Installation"

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If you already installed Victor go directly to the '''[[tutorial]]''' page.
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If you already installed Victor go directly to the '''[[tutorial]]''' page.  
  
==Download==
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'''N.B.''' Remember to set the '''[[#Setting the environment |environment variables]]''' even if you download the compiled version of Victor.
The source code as well as the precompiled version of the software are available in GitHub.  
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You can '''download''' it directly from [[https://github.com/ GitHub]]  
+
  
Alternatively you can '''clone''' Victor into your local repository. Assuming you already have installed the [http://git-scm.com/downloads '''Git software'''], just type:
 
  
  git clone https://github.com/BioComputingUP/Victor.git <your_folder>
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= Download =
 +
The source code as well as the precompiled version of the software are available in GitHub. To get Victor please follow the instructions in the '''[[#Source Code|Source Code]]''' and '''[[#Build|Build]]''' sections. If you are familiar with GitHub you can visit the [https://github.com/BioComputingUP/Victor Victor page].  
  
==Compile==
 
If you successfully got the source code, now you need to compile it. Before compiling, please check that the '''g++ compiler''' is installed in your system and set a couple of environment variables in the '''makefile.global''' or just type the following command, replacing <your_folder> with the Victor main directory and remember to put the tailing "/" to avoid strange errors:
 
  
export VICTOR_ROOT=/<your_folder>/victor/ 
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== Download Build ==
export PATH=$PATH:/<your_folder>/victor/bin/
+
'''N.B.''' Remember to set the '''[[#Setting the environment |environment variables]]''' after the download.<br><br>
 +
A '''precompiled version''' of the software is also available from the GitHub website in the ''Release'' section. Note that the compiled version has been generated in a '''64bit''' environment using '''Ubuntu 14.04''' and '''g++ 4.8.2'''. The link to the page is:
  
Now, to compile the library simply do:
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https://github.com/BioComputingUP/Victor/releases
 +
 
 +
 
 +
== Download Source Code ==
 +
To get the '''source code''' you can clone Victor into your local machine from the command line. Assuming you already have installed the [http://git-scm.com/downloads '''Git software'''], just type in a terminal:
 +
 
 +
git clone https://github.com/BioComputingUP/Victor.git <your_folder>
 +
 
 +
= Compilation =
 +
'''N.B.''' Remember to set the '''[[#Setting the environment |environment variables]]''' after the compilation.<br><br>
 +
 
 +
The compilation requires the "Standard Template Library" STD, and the C++ compiler. According to your environment different packages are necessary:
 +
 
 +
* '''Ubuntu''' (and Debian-derived distributions). Install '''build-essential''' (from the command line ''sudo apt-get install build-essential'').
 +
* '''OSX'''. Install '''Xcode''' (free from the App Store).
 +
* '''CentOS'''. Install '''Development Tools''' (from the command line ''sudo yum group install "Development Tools" '').
 +
 
 +
If you successfully got the source code and installed the required packages, compile it with:
  
 
  make clean
 
  make clean
  make install
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  make
  
After that you should obtain the following '''folder structure''':
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The '''make clean''' ensures the compilation process will start from scratch.
  
<pre>
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After the compilation finishes successfully you should obtain the following list of folders:
bin/            // a copy of all "APPS" executable
+
  
lib/            // libraries
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{| cellspacing="0" border="1" cellpadding="5"
 +
|bin/           
 +
|copy of all "APPS" executables
 +
|-
 +
|lib/             
 +
|libraries
 +
|-
 +
|data/          
 +
|symbolic links to the content of the "Data" folder inside packages
 +
|-
 +
|samples/      
 +
|tutorial examples
 +
|-
 +
|tools/         
 +
|helper classes
 +
|-
 +
|Biopool/       
 +
|Biopool package
 +
|-
 +
|Align2/       
 +
|Align package
 +
|-
 +
|Energy/       
 +
|Energy package
 +
|-
 +
|Lobo/         
 +
|Lobo package
 +
|}
  
data/          // symbolic links to the content of the "Data" folder inside packages
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= Setting the environment =
 +
To make the software operative you need to set a couple of variables in your environment both in the case you are using the precompiled version or the version locally built from source.
  
samples/       // some PDB files for testing purpose
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To set the two variable in Bash just type the following commands, replacing <your_folder> with the Victor main directory. Remember to put the tailing backslash symbol ("/") at the end to avoid strange errors:
  
  tools/         // some helper classes
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  export VICTOR_ROOT=/<your_folder>/Victor/ 
 +
export PATH=$PATH:/<your_folder>/Victor/bin/
  
Biopool/       // the Biopool package
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By this, your current session knows where Victor is installed. However, to make the system permanently aware, also when opening new sessions (terminals), you can just edit your Bash configuration file (usually '''/home/<user_name>/.bashrc''' in Ubuntu). Add the following two lines, replacing <your_folder> with the Victor main directory:
        /APPS
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        /Data
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        /Sources
+
  
  Energy/         // the Energy package
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  export VICTOR_ROOT=/<your_folder>/Victor/
      /APPS
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export PATH=$PATH:/<your_folder>/Victor/bin/
      /Data
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      /Sources
+
  
Lobo/          // the Lobo package
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= Unit Test =
    /APPS
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    /Data
+
    /Sources
+
  
</pre>
+
For information about testing Victor please visit the '''[[Documentation]]''' page.

Latest revision as of 11:27, 12 November 2014

If you already installed Victor go directly to the tutorial page.

N.B. Remember to set the environment variables even if you download the compiled version of Victor.


Download

The source code as well as the precompiled version of the software are available in GitHub. To get Victor please follow the instructions in the Source Code and Build sections. If you are familiar with GitHub you can visit the Victor page.


Download Build

N.B. Remember to set the environment variables after the download.

A precompiled version of the software is also available from the GitHub website in the Release section. Note that the compiled version has been generated in a 64bit environment using Ubuntu 14.04 and g++ 4.8.2. The link to the page is:

https://github.com/BioComputingUP/Victor/releases


Download Source Code

To get the source code you can clone Victor into your local machine from the command line. Assuming you already have installed the Git software, just type in a terminal:

git clone https://github.com/BioComputingUP/Victor.git <your_folder>

Compilation

N.B. Remember to set the environment variables after the compilation.

The compilation requires the "Standard Template Library" STD, and the C++ compiler. According to your environment different packages are necessary:

  • Ubuntu (and Debian-derived distributions). Install build-essential (from the command line sudo apt-get install build-essential).
  • OSX. Install Xcode (free from the App Store).
  • CentOS. Install Development Tools (from the command line sudo yum group install "Development Tools" ).

If you successfully got the source code and installed the required packages, compile it with:

make clean
make

The make clean ensures the compilation process will start from scratch.

After the compilation finishes successfully you should obtain the following list of folders:

bin/ copy of all "APPS" executables
lib/ libraries
data/ symbolic links to the content of the "Data" folder inside packages
samples/ tutorial examples
tools/ helper classes
Biopool/ Biopool package
Align2/ Align package
Energy/ Energy package
Lobo/ Lobo package

Setting the environment

To make the software operative you need to set a couple of variables in your environment both in the case you are using the precompiled version or the version locally built from source.

To set the two variable in Bash just type the following commands, replacing <your_folder> with the Victor main directory. Remember to put the tailing backslash symbol ("/") at the end to avoid strange errors:

export VICTOR_ROOT=/<your_folder>/Victor/  
export PATH=$PATH:/<your_folder>/Victor/bin/

By this, your current session knows where Victor is installed. However, to make the system permanently aware, also when opening new sessions (terminals), you can just edit your Bash configuration file (usually /home/<user_name>/.bashrc in Ubuntu). Add the following two lines, replacing <your_folder> with the Victor main directory:

export VICTOR_ROOT=/<your_folder>/Victor/  
export PATH=$PATH:/<your_folder>/Victor/bin/

Unit Test

For information about testing Victor please visit the Documentation page.