TASSELpy is a Python API for the Java program TASSEL. It provides a number of Python wrappers for the TASSEL classes and functions, allowing the user to seamlessly interact with the TASSEL program in a completely Pythonic way, even though all calculations are completed using the Java Virtual Machine.
TASSEL is primarily used for association mapping and other tasks in quantitiative genetics, although it has a large number of features for various aspects of biological sequence analysis. TASSELpy’s goal is to provide tools that allow convenient scripting of common genetics tasks while taking advantage of the efficiency of the JVM.
TASSELpy’s requirements include those for TASSEL5 (JDK v1.7 or greater), python-javabridge, and numpy. Python-javabridge also requires a C compiler to run.
On MacOSX, there is currently an issue with javabridge using the correct version. For now this can be manually resolved. First, ensure that the JDK 1.7 or greater is installed on your system and that /usr/libexec/java_home points to this JDK. Now perform the following:
curl "https://pypi.python.org/packages/source/j/javabridge/javabridge-1.0.7.tar.gz" -o "javabridge-1.0.7.tar.gz"
tar -xvf javabridge-1.0.7.tar.gz
cd javabridge-1.0.7
Open up the setup.py file in your favorite plain text editor of choice (e.g. emacs, nano), and delete the following lines (should be 97 and 98):
include_dirs += ['/System/Library/Frameworks/JavaVM.framework/Headers']
extra_link_args = ['-framework', 'JavaVM']
Now, replace those deleted lines with these ones (within the same scope):
java_home = subprocess.check_output(['/usr/libexec/java_home']).strip()
include_dirs += [os.path.join(java_home,'include'),
os.path.join(java_home,'include','darwin')]
include_dirs += ['/System/Library/Frameworks/JavaVM.framework/Headers']
extra_link_args = ['-L%s' % os.path.join(java_home,'jre','lib','server'),'-ljvm']
extra_link_args += ['-Wl,-rpath,%s' % os.path.join(java_home,'jre','lib','server')]
On CentOS 6, all dependencies can be installed as follows:
yum install gcc numpy python-devel java-1.7.0-openjdk-devel
curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
python get-pip.py
pip install -U javabridge
On Fedora 19, the dependencies can be installed as follows:
yum install gcc numpy python-devel java-1.7.0-openjdk-devel python-pip openssl
pip install -U javabridge
On Ubuntu 13.10 and Debian 7.0, the dependencies can be installed as follows:
apt-get install openjdk-7-jdk python-pip python-numpy python-dev
pip install -U javabridge
On Windows:
By default, you probably will not have a C compiler installed, so install the Windows SDK 7.1 and .Net Framework 4.0 to perform the compile steps unless there is a preexisting C compiler on your system. Install the Oracle JDK v 1.7 (or v 1.8). Ensure that the paths to pip and python are in your PATH. Now perform the following steps:
Open the Windows SDK command prompt, and provide the following commands:
set MSSdk=1 set DISTUTILS_USE_SDK=1 pip install -U javabridge pip install -U tasselpy