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\begin{document}

\title{Biopython Installation}
\author{Brad Chapman, with other contributors}

\maketitle
\tableofcontents

\section{Purpose and Assumptions}

For those of you familiar with installing python packages and who don't
care for following details instructions can try going to
\ahrefurl{\url{http://biopython.org/wiki/Download}}, installing
the relevant prerequisites, and Biopython.

This document describes installing Biopython on your computer. To make
things as simple as possible, it basically assumes you have nothing
related to Python or Biopython on your computer and want to end up with
a working installation of Biopython when you are finished following
through this documentation. 

Biopython should work on just any operating system where Python works,
so these instructions contain directions for installation on UNIX/Linux,
Windows and Macintosh machines. The directions assume 
that you have permission to install programs on the machine
(root access on UNIX and Administrator privileges on Windows or Mac
machines). While it is certainly possible to install things without
these privileges, this is a serious pain and all the tedious workarounds
aren't something that I'll go into very much in this documentation.

With all this said, hopefully these directions will make it
straightforward to get Biopython installed on your machine so you can
begin using it as quick as possible.

\section{C Compiler}

Although mostly written in Python, Biopython (and some of its dependencies)
include C code, which must be compiled to run. If you are going to be
installing from source you will therefore need a C compiler. However,
in many cases this can be avoided by using pre-compiled packages (which
is what we recommend on Windows).

\subsection{Unix}
We recommend GCC as the C compiler, this is usually available as part
of the standard set of packages on any Unix or Linux system.

\subsection{Mac OS X}
Please install Apple's XCode suite from the App Store, and then from
the Xcode options also install the optional command line utilities.

\subsection{Windows}
We recommend you install Biopython and its dependencies using the
provided pre-compiled Windows Installers. i.e. You don't \emph{need}
a C compiler. See Section~\ref{sec:windows_install} for more details.

\section{Installing Python}

Python is a interpreting, interactive object-oriented programming
language and the home for all things python is
\ahrefurl{\url{http://www.python.org}}. Presumedly you have some idea of
python and what it can do if you are interested in Biopython, but if not
the python website contains tons of documentation and reasons to learn
to program in python.

Biopython is designed to work with Python 2.5 to 2.7 inclusive.
Python 2.7 is the final 2.x series release, and this would be our
recommended version (assuming all other Python libraries you plan
to use support it).

Upgrading bug-fix releases (for example. 2.6.1 to 2.6.2) 
is incredibly easy and won't require any re-installation of libraries.

Upgrading between versions (e.g. 2.6 to 2.7) is more time consuming since you
need to re-install all libraries you have added to python.

As of Biopython 1.62 we officially support Python 3, specifically Python 3.3.
Python 3.0, 3.1 and 3.2 will not be supported.

Let's get started with installation on various platforms.

\subsection{Python installation on UNIX systems}

First, you should go the main python web site and head over to the information
page for the latest python release. At the time of this writing the
latest stable Python 2 release is 2.7.5, which is available from
\ahrefurl{\url{http://www.python.org/download/releases/2.7.5/}}. This page contains links
to all released files for the given release. For UNIX, we'll want to use
the tarred and gzipped file, which is called \verb|Python-2.7.5.tgz| at
the time of this writing.

Download this file and then unpack it with the following command:

\begin{verbatim}
$ tar -zxvf Python-2.7.5.tar.gz
\end{verbatim}

Then enter into the created directory:

\begin{verbatim}
$ cd Python-2.7
\end{verbatim}

Now, start the build process by configuring everything to your system:

\begin{verbatim}
$ ./configure
\end{verbatim}

Build all of the files with:

\begin{verbatim}
$ make
\end{verbatim}

Finally, you'll need to have root permissions on the system and then
install everything:

\begin{verbatim}
$ make install
\end{verbatim}

If there were no errors and everything worked correctly, you should now
be able to type \verb|python| at a command prompt and enter into the
python interpreter:

\begin{verbatim}
$ python
Python 2.7.5 (...)
...
Type "help", "copyright", "credits" or "license" for more information.
>>>
\end{verbatim}

\noindent (The precise version text and details will depend on the version you installed and your operating system.)

\subsubsection{RPM and other Package Manager Installation}

There are a multitude of package manager systems out there for which
python is available. One popular one is the RPM (RedHat Package Manager)
system. Each of these package managing systems has its own quirks and
tricks and I certainly can't pretend to understand them all so I won't
try to describe them all here.

While these package repositories may include Biopython all ready to install,
you will typically want to install Biopython from source to get the very
latest version.

However, there is one general point which it is important to remember
when installing from any of these systems: you need to download and
install the development packages for python. A number of distributions
contain a "basic" python which contains libraries and enough stuff to
run simple python programs. However, they do not contain the python
libraries necessary to build third-party python applications (like
Biopython and it's dependencies). You'll need to install these libraries
and header files, which are often found in a separate package called
\verb|python-devel| or something similar. 

\subsection{Python installation on Windows} 

Installation on Windows is most easily done using handy windows
installers. As described above in the UNIX section, you should go to the
webpage for the current stable version of Python to download this
installer. At the current time, you'd go to
\ahrefurl{\url{http://www.python.org/download/releases/2.7.5/}} and download
\verb|Python-2.7.5.msi|. 

The installer is an executable program, so you only need to double click
it to run it. Then just follow the friendly instructions. On all newer Windows
machines you'll need to have Administrator privileges to do this
installation.

\subsection{Python installation on Mac OS X}

Apple includes python on Mac OS X, and while you can use this many people have
preferred to install the latest version of python as well in parallel. We refer
you to the \ahrefurl{\url{http://www.python.org}} for more details, although
otherwise the UNIX instructions apply.

(See note above about installing XCode to get the compiler tools.)

\section{Installing Biopython dependencies}

Once python is installed, the next step is getting the dependencies
for Biopython installed. Since not all functionality is included in the
main python installation, Biopython needs some support libraries to save
us a lot of work re-writing code that already exists. We try to keep
as few dependencies as possible to make installation as easy as
possible.

\subsection{Numerical Python (NumPy) (strongly recommended)}

The Numerical Python distribution is a fast implementation of arrays and
associated array functionality. This is important for a number of Biopython
modules that deal with number processing (e.g. Bio.Cluster and Bio.PDB).

As of release 1.49, Biopython supports the standard NumPy distribution.
Previous releases instead used the older Numeric module (which is no
longer being maintained).

The main web site for NumPy is:
\ahrefurl{\url{http://numpy.scipy.org/}}.

\subsubsection{UNIX and Mac OS X systems}

You should download the \verb|tar.gz| file, and follow the standard python
build process. Note you will need a C compiler installed (see above):

\begin{verbatim}
$ tar -zxvf numpy-1.7.1.tar.gz
$ cd numpy-1.7.1/
$ python setup.py build
\end{verbatim}

Once it is built, you should become root, and then install it:

\begin{verbatim}
$ python setup.py install
\end{verbatim}

One important note if you use an package system and not installing
NumPy from source: you may also need to
install the header files which are not included with some
packages. As with the main python distribution, this means
you'll need to look for something like \verb|python-numpy-devel| 
and make sure to install this as well as the basic package.

\subsubsection{Windows systems}

We recommend using the NumPy provided windows installers for your installed
version of python. For Python 2.7, at the current time this would be
\verb|numpy-1.7.1-win32-superpack-python2.7.exe|. You should follow the 
now-standard procedure of downloading the installer, double
clicking it and then following the installation instructions. As before,
you will need to have administrator permissions to do this.

\subsubsection{Making sure it installed correctly}

To make sure everything went okay during the install, fire up the python
interpreter and ensure you can import NumPy without any errors:

\begin{verbatim}
$ python2.7
Python 2.7.4 (default, Apr  8 2013, 15:01:09) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>
\end{verbatim}

Note that for the import statement, NumPy should be in lower case!

\subsection{ReportLab (optional)}

The ReportLab package is a library for generating PDF documents. It is
used in the Biopython Graphics modules, which contains basic
functionality for drawing biological objects like chromosomes. If you
are not planning on using this, installing ReportLab is not necessary.
ReportLab in itself is very useful for a number of tasks besides just
Biopython, so you may want to check out
\ahrefurl{\url{http://www.reportlab.org}} before making your decision.

The main download page for ReportLab is
\ahrefurl{\url{http://www.reportlab.org/downloads.html}}. The ReportLab
company has some commercial products as well, but just scroll down their
page to the Open Source software section for the base ReportLab
downloads.

If you want to generate bitmap images, you will also need the ReportLab
module renderPM.  This in turn requires the
\href{http://www.pythonware.com/products/pil/}{Python Imaging Library (PIL)}.

\subsubsection{UNIX and Mac OS X systems}

For UNIX installs, you should download the tarred and gzipped version of
the ReportLab distribution. At the time of this writing, this is called
\verb|ReportLab_2_3.tar.gz|. First, unpack the distribution and change
into the created directory:

\begin{verbatim}
$ gunzip ReportLab_2_3.tar.gz
$ tar -xvpf ReportLab_2_3.tar
$ cd reportlab_2_3/
\end{verbatim}

Once again, ReportLab uses the standard python installation system which
you are probably feeling really comfortable with by now. So, first build
the package:

\begin{verbatim}
$ python setup.py build
\end{verbatim}

Now become root, and install it:

\begin{verbatim}
$ python setup.py install
\end{verbatim}

\subsubsection{Windows systems}

ReportLab now has graphical windows installers.  Nice and easy.

\subsubsection{Making sure it installed correctly}

If reportlab is installed correctly, you should be able to do the
following:

\begin{verbatim}
$ python2.7
Python 2.7.4 (default, Apr  8 2013, 15:01:09) 
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from reportlab.graphics import renderPDF
>>>
\end{verbatim}

Depending on your version of python and what you have installed, you may
get the following warning message: 
\verb|Warn: Python Imaging Library not available|.  This isn't anything
to worry about unless you want to produce bitmap images, since the
Biopython parts that use ReportLab will work just fine without it.

\subsection{Database Access (MySQLdb, ...) (optional)}

The MySQLdb package is a library for accessing MySQL databases.
Biopython includes an accessory module, DocSQL, which provides a convenient
interface to MySQLdb. 
If you are not planning on using Bio.DocSQL, installing
MySQLdb is not necessary.

Additionally, both MySQLdb and psycopg (a PostgreSQL database adaptor)
can be used for accessing BioSQL databases through Biopython
(see \ahrefurl{\url{http://biopython.org/wiki/BioSQL}}). Again if
you are not going to use BioSQL, there shouldn't be any need to install
these modules.

\subsection{mxTextTools (no longer needed)}

Historically this was an important Biopython dependency, used extensively
in a number of parsers.  However, we have gradually phased out its use,
and as of Biopython 1.50, mxTextTools is no longer used at all.

mxTextTools is available along with the entire mx-base system (which
contains a number of other useful utilities as well) and the latest
version is available for download at:
\ahrefurl{\url{http://www.egenix.com/products/python/mxBase/mxTextTools/}}.

\section{Installing Biopython}

\subsection{Obtaining Biopython}
Biopython's internet home is at, naturally enough,  
\ahrefurl{\url{http://www.biopython.org}}. This is the home of all things 
Biopython, so it is the best place to start looking around. 
You have two choices for obtaining Biopython:

\begin{enumerate}

\item Release code -- We made available releases on the download page 
(\ahrefurl{\url{http://biopython.org/wiki/Download}}). 
The releases are also available both as source and as installers 
(windows installers right now), so you have some choices to pick from 
on releases if you prefer not to deal with source code directly.

\item git -- The current working copy of the Biopython sources is available
via git hosted on github  -- \ahrefurl{\url{http://github.com/biopython/biopython}}).
Concise instructions for accessing this copy are available at
\ahrefurl{\url{http://biopython.org/wiki/SourceCode}}. Our code in git
is normally quite stable but there is always the caveat that the code
there is under development.

\end{enumerate}

Based on which way you choose, you'll need to follow one of the following installation options. Read on for the platform you are working on.

\subsection{Installing on UNIX and Mac OS X}
\label{sec:unix_install}

\subsubsection{Installation from source on UNIX and Mac OS X}

Biopython uses Distutils, the standard python installation package, for
its installation. If you read the install instructions above you are
already quite familiar with its workings. Distutils comes standard with 
Python 1.6 and beyond.

Now that we've got what we need, let's get into the installation:

\begin{enumerate}

\item First you need to unpack the distribution. If you got the git version, you are all set to go and can skip on ahead. Otherwise, you'll need to unpack it. On UN*X machines, a tar.gz package is provided, which you can unpack with \verb|tar -xzvpf biopython-X.X.tar.gz|. A zip file is also provided for other platforms.

\item Now that everything is unpacked, move into the \verb| biopython*| directory (this will just be \verb|biopython| for git users, and will be \verb|biopython-X.X| for those using a packaged download). 

\item Now you are ready for your one step install -- \verb|python setup.py install|. This performs the default install, and will put Biopython into the \verb|site-packages| directory of your python library tree (on my machine this is \verb|/usr/local/lib/python2.4/site-packages|). You will have to have permissions to write to this directory, so you'll need to have root access on the machine.

\begin{enumerate}

\item This install requires that you have the python source available. You can check this by looking for \verb|Python.h| and \verb|config.h| in some place like \verb|/usr/local/include/python2.5|. If you installed python with RPMs or 
some other packaging system, this means you'll also have to install the
header files. This requires installing the python development libraries
as well (normally called something like \verb|python-devel-2.5.rpm|).

\item The distutils setup process allows you to do some customization of your install so you don't have to stick everything in the default location (in case you don't have write permissions there, or just want to test Biopython out). You have quite a few choices, which are covered in detail in the distutils installation manual (\ahrefurl{\url{http://www.python.org/sigs/distutils-sig/doc/inst/inst.html}}), specifically in the Alternative installation section. For example, to install Biopython into your home directory, you need to type \verb|python setup.py install --home=$HOME|. This will install the package into someplace like \verb|$HOME/lib/python2.5/site-packages|. You'll need to subsequently modify the \verb|PYTHONPATH| environmental variable to include this directory so python will be able to find the installation.

\end{enumerate}

\item That's it! Biopython is installed. Wasn't that easy? Now let's check and make sure it worked properly. Skip on ahead to section~\ref{sec:is_working}.

\end{enumerate}

\subsubsection{Using the Python package index}

Another simple option is to use the Python package index
(\ahrefurl{\url{http://pypi.python.org/pypi}}) with the \verb|easy_install|
command:

\begin{verbatim}
$ easy_install -f http://biopython.org/DIST/ biopython
\end{verbatim}

If Python is installed in the standard location, you will need administrator
privileges to do this; the \verb|sudo| command works well:

\begin{verbatim}
$ sudo easy_install -f http://biopython.org/DIST/ biopython
\end{verbatim}

% FreeBSD port not up to date
% \subsubsection{Installation on FreeBSD}
% 
% Johann Visagie has been kind enough to create (and keep updated) a FreeBSD port of Biopython. Thanks to the wonders of the ports system, this means that all you need to do to install Biopython on FreeBSD is do the following as root:
% 
% \begin{verbatim}
% cd /usr/ports/biology/py-biopython
% make install
% \end{verbatim}
% 
% And voila! It's installed. 
% 
% If you want more information on FreeBSD and things, Johann has written a nice primer for his FreeBSD EMBOSS port. This has lots of generally useful information, such as how to keep your ports tree up to date. If you are new to FreeBSD, you should definitely check it out at \ahrefurl{\url{ftp://ftp.no.embnet.org/pub/EMBOSS-extras/EMBOSS-FreeBSD-HOWTO.txt}}.

\subsubsection{Installation on Mac OS X using the fink package manager}

Instead of installing from source, on Mac OS X you can also use the fink package manager, see \ahrefurl{\url{http://fink.sf.net}}. Fink should take care of downloading the source code and installing all needed packages for Biopython, including Python itself. Once you have installed fink, you can install biopython using:

\begin{verbatim}
$ fink install biopython-pyXX
\end{verbatim}

\noindent where XX is the python version you would like to use. Currently, python 2.4, 2.5, and 2.6 are available through fink on Mac OS X 10.4, so you would have to replace XX with 24, 25, or 26, respectively. Most likely, you will have to enable the unstable tree of fink in order to install the most recent versions of the package, see also this item in the Fink FAQ: \url{http://fink.sourceforge.net/faq/usage-fink.php#unstable}. Note that 'unstable' doesn't mean that a package won't work, but only that there has not been feedback to the fink team from users.

\subsubsection{Installation on UNIX systems using RPMs}

Warning. Right now we're not making RPMs for biopython (because I
stopped using an RPM system, basically). If anyone wants to pick this
up, or feels especially strongly that they'd like RPMs, please let us
know.

To simplify things for people running RPM-based systems, biopython can
also be installed via the RPM system. Additionally, this saves the 
necessity of having a C compiler to install biopython. 

Installing Biopython from a RPM package should be much the same process as used for other RPMs. If you need general information about how RPMs work, the best place to go is \ahrefurl{\url{http://www.rpm.org}}.

To install it, you should just need to do:

\begin{verbatim}
$ rpm -i your_biopython.rpm
\end{verbatim}

To see what you installed try doing \verb|rpm -qpl your_biopython.rpm| which will list all of the installed files.

RPMs do not install the documentation, tests, or example code, so you might want to also grab a source distribution, so you can use these resources (and also look at the source code if you want to).

\subsection{Installing with a Windows Installer}

Installing things on Windows with the installer should be really easy (hey, that's why they've got graphical installers, right?). You should just need to download the \verb|Biopython-version.exe| installer from biopython web site. Then you just need to double click and voila, a nice little installer will come up and you can stick the libraries where you need to. No need for a C compiler or anything fancy. You will need to have Administrator privileges on the machine to do the installation.

This does not install the documentation, tests, example code or source code, so it is probably also a good idea to download the zip file containing this so you can test your installation and learn how to use it.

\subsection{Installing from source on Windows}
\label{sec:windows_install}

This section deals with installing the source (i.~e.~from git or from a source zip file) on a Windows machine. Much of the information from the UNIX install applies here, so it would be good to read section~\ref{sec:unix_install} before starting.  You will need a suitable C compiler.
What you choose may depend on your version of Python.

For Python 2.6 we currently use Microsoft's free VC++ 2008 Express Edition from \ahrefurl{\url{http://www.microsoft.com/express/download/}}, installation of this is pretty simple.  Then go to the Biopython source directory and run:

\begin{verbatim}
c:\python26\python setup.py build
c:\python26\python setup.py test
c:\python26\python setup.py install
\end{verbatim}

For older versions of Python, we use mingw32 installed from cygwin (\ahrefurl{\url{http://www.cygwin.com}}).  Once everything is setup (which is a bit complicated), you would again get the source, and from that directory run:

\begin{verbatim}
c:\python25\python setup.py build --compiler=mingw32
c:\python25\python setup.py test
c:\python25\python setup.py install
\end{verbatim}

Previously (back on Python 2.0), Brad has also managed to use Borland's free C++ compiler (available from \ahrefurl{\url{http://www.inprise.com/bcppbuilder/freecompiler/}}), but this required extra work.

Now that you've got everything installed, carry on ahead to section~\ref{sec:is_working} to make sure everything worked.

\section{Making sure everything worked}
\label{sec:is_working}

First, we'll just do a quick test to make sure Biopython is installed correctly. The most important thing is that python can find the biopython installation. Biopython installs into top level \verb|Bio| and \verb|BioSQL| directories, so you'll want to make sure these directories are located in a directory specified 
in your\verb| $PYTHONPATH| environmental variable. If you used the default install, this shouldn't be a problem, but if not, you'll need to set the \verb|PYTHONPATH| with something like \verb|export PYTHONPATH = $PYTHONPATH':/directory/where/you/put/Biopython'| (on UNIX). Now that we think we are ready, fire up your python interpreter and follow along with the following code:

\begin{verbatim}
$ python
Python 2.5 (r25:51908, Nov 23 2006, 18:40:28) 
[GCC 4.1.1 20061011 (Red Hat 4.1.1-30)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet.IUPAC import unambiguous_dna
>>> new_seq = Seq('GATCAGAAG', unambiguous_dna)
>>> new_seq[0:2]
Seq('GA', IUPACUnambiguousDNA())
>>> new_seq.translate()
Seq('DQK', IUPACProtein())
>>>
\end{verbatim}

If this worked properly, then it looks like Biopython is in a happy place where python can find it, so now you might want to do some more rigorous tests. The \verb|Tests| directory inside the distribution contains a number of tests you can run to make sure all of the different parts of biopython are working. These should all work just by running \verb|python test_WhateverTheTestIs.py|. 

If you didn't do this earlier, you should also all of our tests. To do this, you just need to be in the source code installation directory and type:

\begin{verbatim}
$ python setup.py test
\end{verbatim}

You can also run them by typing \verb|python run_tests.py| in the Tests sub directory.
See the main Tutorial for further details (there is a whole chapter on the test framework).

If you've made it this far, you've gotten Biopython installed and running.
Congratulations!

\section{Third Party Tools}

Note that Biopython includes support for interfacing with or parsing the output from a number of third party command line tools.  These are not required to install Biopython, but may be of interest.  This includes:

\begin{itemize}
\item NCBI Standalone BLAST, which can used with the \verb|Bio.Blast| module and parsed with the \verb|Bio.SearchIO| module.
\item EMBOSS tools, which can be invoked using the \verb|Bio.Emboss| module.  The \verb|Bio.AlignIO| module can also parse some alignment formats output by the EMBOSS suite.
\item ClustalW, which can be parsed using \verb|Bio.AlignIO| and invoked using the \verb|Bio.Align.Applications| module.
\item SIMCOAL2 and FDist tools for population genetics can be used via the \verb|Bio.PopGen| module.
\item Bill Pearson's FASTA tools output can be parsed using the \verb|Bio.AlignIO| and \verb|Bio.SearchIO| module.
\item Wise2 includes the useful tool dnal.
\end{itemize}

\noindent
See also the listing on \ahrefurl{\url{http://biopython.org/wiki/Download}} which should include URLs for these tools, and may also be more up to date.

\section{Notes for installing with non-administrator permissions}

Although I mentioned above that I wouldn't go much into installing in
non-root directories, if you are stuck installing
Biopython and it's dependencies into your home directory here are a
few notes and tricks to keep you going:

\begin{itemize}

  \item Building some C modules, such as \verb|Bio.Cluster| require that 
    the NumPy include files (normally installed in
    \verb|your_dir/include/python/Numeric|) be available. If the
    compiler can't find these directories you'll normally get an error
    like:

    \begin{verbatim}
Bio/Cluster/clustermodule.c:2: NumpPy/arrayobject.h: No such file or directory
    \end{verbatim}

    Followed by a long messy list of syntax errors. To fix this, you'll
    have to edit the \verb|setup.py| file to let it know where the
    include directories are located. Look for the line in
    \verb|setup.py| that looks like:

    \begin{verbatim}
    include_dirs=["Bio/Cluster"]
    \end{verbatim}

    and adjust it so that it includes the include directory where the
    NumPy libraries were installed:
    
    \begin{verbatim}
    include_dirs=["Bio/Cluster", "your_dir/include/python"]
    \end{verbatim}

    Then you should be able to install everything happily.

\end{itemize}

Yes, it's a bit of a mess installing lots of packages in non-standard
locations. The best solution is to talk with your friendly system
administrator and get them to assist with the installation of at least
the required packages (they are generally quite useful for any python
install) before going ahead with Biopython installation.

\end{document}