Difference between revisions of "Installation"

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== Development version ==
 
== Development version ==
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Remark: [http://wikipedia.org/wiki/git git] and [http://wikipedia.org/wiki/CMake CMake] are needed to download and compile the source files (<tt>git</tt> and <tt>cmake</tt> package in Ubuntu/Debian repositories).
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Remark: Installing Bio++ in a custom location greatly helps in compiling and running programs depending on different Bio++ versions. For more information on how to compile/run Bio++ dependent programs, see the [[Category:Usage|Usage]] pages.
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This section demonstrates how to download the sources in <tt>$HOME/local/bpp/dev/sources</tt> and install the libraries in <tt>$HOME/local/bpp/dev/lib</tt> and <tt>$HOME/local/bpp/dev/include</tt>.
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We start by creating the directory :
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<source lang="bash">
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bpp_dir=$HOME/local/bpp/dev/
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mkdir -p $bpp_dir/sources
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</source>
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===== Getting the source files =====
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This is done with <tt>git</tt>.
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You do not need to download all components of the Bio++ library. Namely, the <tt>bpp-core</tt> and <tt>bpp-seq</tt> components required by all others, which are otherwise independent.
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<source lang="bash">
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cd $bpp_dir/sources
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git clone http://biopp.univ-montp2.fr/git/bpp-core
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git clone http://biopp.univ-montp2.fr/git/bpp-seq
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git clone http://biopp.univ-montp2.fr/git/bpp-phyl
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git clone http://biopp.univ-montp2.fr/git/bpp-popgen
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</source>
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At this point our <source lang="bash">$bpp_dir/sources</source> should contain four subdirectories.
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===== Compiling and installing =====
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All desired components must be compiled successively.
  
 
== Older versions ==
 
== Older versions ==
  
 
See [[Bio++ Versions]].
 
See [[Bio++ Versions]].

Revision as of 16:51, 30 June 2012

How to install Bio++. See also Installation (old page).

Lastest version : Bio++ 2.0

Ubuntu/Debian packages

Bio++ 2.0 packages (libbpp-core, libbpp-seq, etc.) are available in the Ubuntu and Debian standard repositories. They can be installed using your usual package/program manager.

Warning: as of June 30, 2012, there is an issue with the Ubuntu popgen package. If you want to use this part of the library, please use the package from the custom repository instead, or compile from source, or switch to the development version.

Ubuntu/Debian packages (custom repository)

A local repository is available for architectures i386 and amd64, containing additional programs built against the libraries.

Use your favorite apt manager to add the following line to your sources.list :

deb http://biopp.univ-montp2.fr/repos/apt/debian Squeeze main

You will also need to add the key that was used to sign the packages : <source lang="bash"> wget http://biopp.univ-montp2.fr/repos/apt/conf/biopp.gpg.key sudo apt-key add biopp.gpg.key </source>

Reload the packages list and then look for "Bio++" packages. That's all!

RPM packages

RPM packages are available at http://download.opensuse.org/repositories/home:/jdutheil:/Bio++/.

MacOS X

DMG packages are available at http://biopp.univ-montp2.fr/repos/dmg/ (compiled with a MacIntel computer).

Compiling from source

Compiling from source is necessary when superuser rights are not available or to install Bio++ to a non-standard location (useful when several Bio++ versions coexist on a system).

Remark: CMake is needed to compile the sources (cmake package in Ubuntu/Debian repositories).

Compiling from source : the automatic way

The easiest way to compile from source is to download the 2.0 automatic installer, edit the script header to match your system, and run it.

For instance, to download the sources in $HOME/local/bpp2.0 and install the libraries in $HOME/local/lib and $HOME/local/include, one would enter : <source lang="bash"> mkdir $HOME/local $HOME/local/bpp2.0 cd $HOME/local/bpp2.0 wget http://biopp.univ-montp2.fr/Download/bpp-setup.sh chmod +x bpp-setup.sh gedit bpp-setup.sh # set PATH_INSTALL to $HOME/local/, on line 16 ./bpp-setup.sh </source>

Compiling from source : the manual way

Download the source archives individually (see Bio++ Versions). The compilation procedure is then the same as for compiling the development version.

Development version

Remark: git and CMake are needed to download and compile the source files (git and cmake package in Ubuntu/Debian repositories).

Remark: Installing Bio++ in a custom location greatly helps in compiling and running programs depending on different Bio++ versions. For more information on how to compile/run Bio++ dependent programs, see the pages.


This section demonstrates how to download the sources in $HOME/local/bpp/dev/sources and install the libraries in $HOME/local/bpp/dev/lib and $HOME/local/bpp/dev/include.


We start by creating the directory : <source lang="bash"> bpp_dir=$HOME/local/bpp/dev/ mkdir -p $bpp_dir/sources </source>

Getting the source files

This is done with git.

You do not need to download all components of the Bio++ library. Namely, the bpp-core and bpp-seq components required by all others, which are otherwise independent.

<source lang="bash"> cd $bpp_dir/sources git clone http://biopp.univ-montp2.fr/git/bpp-core git clone http://biopp.univ-montp2.fr/git/bpp-seq git clone http://biopp.univ-montp2.fr/git/bpp-phyl git clone http://biopp.univ-montp2.fr/git/bpp-popgen </source>

At this point our <source lang="bash">$bpp_dir/sources</source> should contain four subdirectories.

Compiling and installing

All desired components must be compiled successively.

Older versions

See Bio++ Versions.