Installation of PRANK

 
Back to PRANK home.
 

Automatic check for new versions of PRANK

PRANK includes an option to easily check if program updates are available. With command:

 

prank -version

 

the PRANK checks for updates and lists the changes in the new version.
 

Pre-compiled executables for Windows

The pre-compiled executables are available in the downloads folder.

 

It is recommended to place the unpacked content of the zip file to the directory "Program Files". Here we assume that the file path to the directory "prank" is C:\Program Files\prank.

 

For the ease of use, it is recommended to add the directory prank/bin permanently to the system path. On Windows 7, this can be done through the following steps:

 

  • open "Control Panel"
  • choose "System"
  • on the left panel, choose "Advanced system settings"
  • on the new window, click "Environment Variables"
  • find "Path" in the lower field, select it and click "Edit"
  • leave the existing content intact and add ;C:\"Program Files"\prank in the end of the field "Variable value"
  • click "OK" three times and close "Control Panel"

 

If you now open Command Prompt and write prank, the program should run and show the options list.

 

The executable has been compiled and tested on Windows 7 (32bit) system.

Hints for using PRANK on Windows

PRANK is used through commands given in Command Prompt. For those not familiar with moving around files, the following workflow may be useful.

 

  • open "Command Prompt" from "All Programs" -> "Accessories"
  • in Command Prompt, type commands

    •  

    mkdir analysis
cd analysis
explorer .

     

  • drag and drop your alignment input file(s) to the Explorer window that was opened
  • in Command Prompt, run PRANK as prank -d=myfile [other options]
  • once finished, the result files will appear in the Explorer window

 

Pre-compiled executables for Mac OSX

The pre-compiled executables are available in the downloads folder.

 

The PRANK executable for Mac has been compiled on OSX 10.8. The package contains the PRANK executable and its manual page (read it with command man ./prank/prank.1) as well as BppAncestor, Exonerate and MAFFT executables and the necessary files for those to work correctly.

 

The PRANK package file can be downloaded and unpacked using graphical software. With the command line, the same can be done with the commands:

 

mkdir ~/programs
cd ~/programs
curl -O http://wasabiapp.org/download/prank/prank.osx64.140603.tgz
tar xvzf prank.osx64.140603.tgz
./prank/bin/prank

 

For the ease of use, it is recommended to add the directory prank/bin to the system path or copy its content to a such directory (such as ~/bin or /usr/local/bin). This can be done with commands similar to these:

 

echo "export PATH=$PATH:/Users/$USER/programs/prank/bin" >> ~/.bash_profile

 

or

 

cp -R /Users/$USER/programs/prank/bin/* ~/bin/

 

Note that if the executables are moved or copied, the directory structure (bin/mafftlib) and the location of library dependencies have to be retained.

Pre-compiled executables for Linux

The pre-compiled executables are available in the downloads folder.

 

The PRANK executable for Linux has been compiled on Red Hat 5.10 (64bit) and confirmed to work also on Ubuntu 13.10 and CentOS 6.5. The package contains the PRANK executable and its manual page (read it with command man ./prank/prank.1) as well as BppAncestor, Exonerate and MAFFT executables and the necessary files for those to work correctly.

 

Using the command line, the PRANK executable for Linux can be downloaded and unpacked with the commands:

 

mkdir ~/programs
cd ~/programs
wget http://wasabiapp.org/download/prank/prank.linux64.140603.tgz
tar prank.linux64.140603.tgz
./prank/bin/prank

 

For the ease of use, it is recommended to add the directory prank/bin to the system path or copy its content to a such directory (such as ~/bin or /usr/local/bin). This can be done with commands similar to these:

 

echo "export PATH=$PATH:/home/$USER/programs/prank/bin" >> ~/.bash_profile

 

or

 

cp -R /home/$USER/programs/prank/bin/* ~/bin/

 

Note that if the executables of the bundled version are moved or copied, the directory structure (bin/lib) and the location of library dependencies have to be retained.

Installation of PRANK from source code

You can download a snapshot of the PRANK code from the downloads folder and get the latest version using git as explained on the source code page. On command line, the process looks like this (tested on Linux and MacOSX):

 

wget http://wasabiapp.org/download/prank/prank.source.140603.tgz
# OR
curl -O http://wasabiapp.org/download/prank/prank.source.140603.tgz

tar xvzf prank.source.140603.tgz
cd prank-msa/src
make
./prank

[ cp prank ~/bin ]
[ sudo cp prank /usr/bin ]

 

or

 

git clone https://github.com/ariloytynoja/prank-msa.git 
cd prank-msa/src
make
./prank

[ cp prank ~/bin ]
[ sudo cp prank /usr/bin ]

 

On Windows, the PRANK source code has been verified to compile on the Cygwin environment.

Optional: Installation of MAFFT, Exonerate and BppAncestor

For the fast guide tree estimation, alignment anchoring and ancestral reconstruction to work, you need to have MAFFT, Exonerate and BppAncestor installed and on the execution path. You can download the MAFFT source code from http://www.ebi.ac.uk/~guy/exonerate/ and the Exonerate source code from http://mafft.cbrc.jp/alignment/software/ and follow the instructions for their installation. On many popular Linux distributions MAFFT and Exonerate are available in the software repository and can be installed pre-compiled. On Ubuntu, that is done with the following commands:

 

sudo apt-get install mafft
sudo apt-get install exonerate

 

Because of dependencies in Exonerate, also on MacOSX the installation is easier with a package management system such as Homebrew. On OSX 10.7, Exonerate can be installed with the following commands:

 

sudo /usr/bin/ruby -e "$(curl -fsSL https://raw.github.com/gist/323731)"
sudo brew install pkg-config
sudo brew install exonerate

 

See http://mxcl.github.com/homebrew/ for further details.

 

BppSuite is provided as pre-compiled binaries for several platforms at http://home.gna.org/bppsuite/ and is also available in repositories of some popular Linux distros. Unfortunately, the version of BppAncestor provided there probably contains a critical bug and cannot be used. The commands below compile the program suite against the latest version of the Bpp libraries.

 

mkdir bppsuite
cd bppsuite/
bpp_dir=pwd

mkdir sources 
cd 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/bppsuite


cd bpp-core/
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir -DCMAKE_LIBRARY_PATH=$bpp_dir/lib -DCMAKE_INCLUDE_PATH=$bpp_dir/include -D BUILD_TESTING=FALSE -DCMAKE_EXE_LINKER_FLAGS=-static ./
make
make install

cd ../bpp-seq/
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir -DCMAKE_LIBRARY_PATH=$bpp_dir/lib -DCMAKE_INCLUDE_PATH=$bpp_dir/include -D BUILD_TESTING=FALSE -DCMAKE_EXE_LINKER_FLAGS=-static ./
make
make install

cd ../bpp-phyl/
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir -DCMAKE_LIBRARY_PATH=$bpp_dir/lib -DCMAKE_INCLUDE_PATH=$bpp_dir/include -D BUILD_TESTING=FALSE -DCMAKE_EXE_LINKER_FLAGS=-static ./
make
make install

cd ../bppsuite/
cmake . -DCMAKE_PREFIX_PATH=$bpp_dir -DCMAKE_INSTALL_PREFIX=$bpp_dir -DCMAKE_EXE_LINKER_FLAGS=-static -DBUILD_STATIC=true
make
make install

cd ../../bin/
ls |xargs strip