Prequisites and installation

Prequisites

To use HTSeq, you need at least version 2.5 of Python (Python 3 does not work yet), together with NumPy, a commonly used Python package for numerical calculations. Mac and Linux users will find that this is often pre-installed. (To check whether you have a working NumPy installation, start Python and simply type import numpy. If you do not get an error, NumPy is available. Users of Debian and Ubuntu Linux should install the package python-numpy.)

Download

HTSeq is available from the Python Package Index (PyPI).

Download HTSeq from the

HTSeq package download page on PyPI,

where you will find various version of the package. Either pick a binary archive suitable for your operation system and Python version, or download the source tarball, which should work with all supported operating systems and Python versions.

Installing a binary package

For Windows, the binary package contains an automatic installer, Simply execute it.

If you have a binary package (not containing a subdirectory called src) for Linux or MacOS, unpack it, open a terminal and type, in the unpacked directory,

python setup.py install

If you do not have write permission for Python’s site-package directory, you can install it locally in your home directory as follows:

Python 2.6 users simply type

python setup.py install --user

to get it installed in a place in your home directory (typically ~/.local) where Python will find it.

For a local installation with Python 2.5, you have to specify a place where to install it to:

python setup.py install --home <some_path>

and then tell Python (every time before using HTSeq) where to look for it by setting the environment variable PYTHONPATH:

export PYTHONPATH=$PYTHONPATH:<some_path>/lib/python

To test your installation, simply start Python (not in the directory with setup.py) and type import HTSeq. No error message should appear.

If you have problems with the installation, please do not hesitate to contact me (anders at embl dot de).

Installing a source package

If you have a source package (containing a subdirectory called src), you need to first build the package before installing it. For this, make sure you have the GNU tool chain and the Python header files installed:

• On a Mac, you need to install XCode (available from the Apple web site or from your second Mac OS X install CD).
• On Ubuntu or Debian Linux, install the build-essential and the python-dev package. For other Linux distributions, similar packages are available.
• On MS Windows, MinGW is a commonly used build environment. Using it may be a bit tricky, so use a binary package if possible. If non is available, see below for detailed instructions.

Unpack the source package, open a terminal, cd into the unpacked directory, and type

python setup.py build

Afterwards, proceed as with the binary package.

Installation of a source package on MS Windows

If the current version is not available as binary package for Windows, either ask me to build a Windows package, or proceed as follows:

• In addition to Python and numpy, also install MinGW.

• Download the source package and unpack it (e.g., with 7-zip) onto your desktop.

• Start a command line terminal and type the following commands (substituting paths where they are different on your system):

  cd \Documents and Settings\anders\Desktop\HTSeq-0.4.4
  PATH=%PATH%;C:\Python26;C:\MinGW\bin
  python setup.py build --compiler=mingw32
  python setup.py install