Difference between revisions of "BppSuite"

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(Download: Renaming into "Installation" ; minor changes)
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BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.  
 
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.  
  
== Download ==
+
== Installation ==
  
 
=== Standalone executables ===
 
=== Standalone executables ===
  
 
Standalone executables are available for [http://biopp.univ-montp2.fr/repos/exe/lin32/ linux32], [http://biopp.univ-montp2.fr/repos/exe/lin64/ linux64], [http://biopp.univ-montp2.fr/repos/exe/win32/ win32], [http://biopp.univ-montp2.fr/repos/exe/win64/ win64] and [http://biopp.univ-montp2.fr/repos/exe/mac/ Mac].
 
Standalone executables are available for [http://biopp.univ-montp2.fr/repos/exe/lin32/ linux32], [http://biopp.univ-montp2.fr/repos/exe/lin64/ linux64], [http://biopp.univ-montp2.fr/repos/exe/win32/ win32], [http://biopp.univ-montp2.fr/repos/exe/win64/ win64] and [http://biopp.univ-montp2.fr/repos/exe/mac/ Mac].
 
  
 
=== From source files ===
 
=== From source files ===
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</source>
 
</source>
  
==== Installation ====
+
===== Compiling =====
  
 
Bio++ libraries shoud be installed beforehand, for example in <tt>$bpp_dir</tt>.
 
Bio++ libraries shoud be installed beforehand, for example in <tt>$bpp_dir</tt>.
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cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation
 
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation
 
make # compile
 
make # compile
make install # move files to the installation directory
+
make install # move files to the installation directory (this will create a $bpp_dir/bin/ directory)
 
</source>
 
</source>
  
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* Without the option <tt>-DCMAKE_INSTALL_PREFIX=$bpp_dir</tt>, the standard <tt>/usr/local</tt> directory will be used, and the executables installed in  <tt>/usr/local/bin</tt>, a location which requires superuser access rights.
 
* Without the option <tt>-DCMAKE_INSTALL_PREFIX=$bpp_dir</tt>, the standard <tt>/usr/local</tt> directory will be used, and the executables installed in  <tt>/usr/local/bin</tt>, a location which requires superuser access rights.
  
==== Usage ====
+
===== Usage =====
  
 
Bppsuite executables should know where the dynamic libraries are.  A way to check it is the command:
 
Bppsuite executables should know where the dynamic libraries are.  A way to check it is the command:
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(and source this  file or relog).
 
(and source this  file or relog).
  
=== Documentation ===
+
===== Documentation =====
  
 
You can also generate the pdf documentation by typing :
 
You can also generate the pdf documentation by typing :

Revision as of 14:55, 8 August 2013


BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

Installation

Standalone executables

Standalone executables are available for linux32, linux64, win32, win64 and Mac.

From source files

Getting the sources

This is done with git, for example in directory $bpp_dir:

<source lang="bash"> cd $bpp_dir git clone http://biopp.univ-montp2.fr/git/bppsuite </source>

Compiling

Bio++ libraries shoud be installed beforehand, for example in $bpp_dir.

<source lang="bash"> cd bppsuite cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation make # compile make install # move files to the installation directory (this will create a $bpp_dir/bin/ directory) </source>

That's it ! The executables are now installed in $bpp_dir/bin. For more information on how to compile and run Bio++ dependent programs, see the Usage pages.

  • Without the option -DCMAKE_INSTALL_PREFIX=$bpp_dir, the standard /usr/local directory will be used, and the executables installed in /usr/local/bin, a location which requires superuser access rights.
Usage

Bppsuite executables should know where the dynamic libraries are. A way to check it is the command:

<source lang="bash"> ldd $bpp_dir$/bin/bppml </source>

To configure this, set in the .bashrc the environment variable :

<source lang="bash"> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$bpp_dir </source>

(and source this file or relog).

Documentation

You can also generate the pdf documentation by typing :

<source lang="bash"> make pdf </source>

Examples

Many examples are available in the subdirectory of Examples.

Documentation

Documentation can be found at http://biopp.univ-montp2.fr/manual/html/bppsuite/.