TADbit requires python >= 2.6 as well as several dependencies that are listed below.
Required:
apt-get install python-scipy
apt-get install python-numpy
Optional packages (but highly recommended):
apt-get install python-matplotlib
.. note:: Alternative install, you can install python-setuptools and use easy_install to get these packages (e.g. "easy_install scipy
").
The three-dimensional (3D) structure of a given genomic region is done via the IMP package. TADbit has been tested with IMP version 2.0.1 and IMP version 2.1.1 (recommended IMP versions to be installed). The installation procedure reported in this manual describes how to install IMP on Ubuntu machines (installation tested on Ubuntu versions 12.04, 13.04 and 14.04). However, we do not provide support for installing IMP; installation instructions for IMP can be found on the IMP website (http://salilab.org/imp/nightly/doc/html/).
Install the required libraries:
sudo apt-get install cmake
sudo apt-get install libboost1.49-all-dev
sudo apt-get install libhdf5-dev
sudo apt-get install swig
sudo apt-get install libcgal-dev
sudo apt-get install python-dev
.. note::
For Ubuntu 13.10 libboost1.53-all-dev should be installed instead. For Ubuntu 14.04 libboost1.54-all-dev should be installed instead.
Download the IMP tarball file from http://salilab.org/imp/ and uncompress it:
wget http://salilab.org/imp/get.php?pkg=2.0.1/download/imp-2.0.1.tar.gz -O imp-2.0.1.tar.gz
tar xzvf imp-2.0.1.tar.gz
Move into the IMP directory and compile the code (Note: the -j
option stands for the number of CPUs you want to assign to the compiler; the higher the faster).
cd imp-2.0.1
cmake . -DCMAKE_BUILD_TYPE=Release -DIMP_MAX_CHECKS=NONE -DIMP_MAX_LOG=SILENT
make -j4
Once the compilation has finished, open the file setup_environment.sh in your IMP directory and copy the first lines into your ~/.bashrc
file (if this file in not present in your home directory, create it). These lines should look like:
LD_LIBRARY_PATH="/SOMETHING/imp-2.0.1/lib:/SOMETHING/imp-2.0.1/lib:/SOMETHING/imp-2.0.1/src/dependency/RMF/:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
PYTHONPATH="/SOMETHING/imp-2.0.1/lib:/SOMETHING/imp-2.0.1/lib:/SOMETHING/imp-2.0.1/src/dependency/RMF/:$PYTHONPATH"
export PYTHONPATH
MCL is the program used for clustering the 3D models generated by IMP. It can be downloaded from http://micans.org/mcl/; on Debian/Ubuntu machines it can be automatically installed with:
sudo apt-get install mcl
Note: if the MCL executable is not found by TADbit, an alternative clustering method will be used. Nevertheless we strongly recommend to use MCL.
Chimera is a program used for visualization and analysis of molecular structures. It is used in TADbit to visualize the generated 3D models. Chimera is available at: http://www.cgl.ucsf.edu/chimera/
This software is only needed for the visualization of 3D models from inside TADbit.
TADbit provides a wrapper for the LiftOver tool [Fujita2011]_ (download it from: http://hgdownload.cse.ucsc.edu/admin/exe/ ).
This can be used to ease the conversion of genomic TAD coordinates (e.g.: to align human TADs with mouse TADs).
Once all the needed library/software have been installed, TADbit can be downloaded, unpacked and installed as:
wget https://github.com/3DGenomes/tadbit/archive/master.zip -O tadbit.zip
unzip tadbit.zip
cd tadbit-master
sudo python setup.py install
sudo PYTHONPATH=$PYTHONPATH python setup.py install
Finally, run the test script to check that the installation completed successfully.
To do so, move to the test directory and run:
cd test
python test_all.py