Please contact us on our Support group if you experience any problems.
HINT uses python library PyX to automatically combine the line plots of raw signal and bias corrected signal for a particular motif. This library can be installed by pip:
pip install pyx==0.12.1
For more information, please check PyX website.
The HINT Tool will automatically install all other python package requirements. However, we highly recommend that you pre-install Cython, numpy and scipy. It is also recommended to install scikit-learn before performing the installation of HINT. This can easily be performed with:
pip install -U scikit-learn
If you experience any problems with the installation regarding the package requirements, you can try to install these packages individually (please visit their website listed bellow for more information). The package requirements for the most current version is:
- Python >= 2.7
- Numpy >= 1.4.0
- Scipy >= 0.7.0
- scikit-learn >= 0.14
- hmmlearn >= 0.1.1
- Pysam >= 0.7.5
- ngslib >= 1.1.14
Also, in case you want to save storage space and work with bigbed format insted of bed format (using –bigbed option), you must download the script bedToBigBed from the UCSC utilities website (linux x86) and place them in on of the paths in your $PATH variable (UNIX systems). To verify the list of paths in this variable please type the command:
In the introduction it was explained how to install the package in a fast way if you have superuser privileges. However, if you don’t have such privileges (for instance, you are running the tool in a server) you can install the package manually using the prefix scheme. This can be easily performed (for python version X.Y) by typing the following command:
export PATH=$PATH:~/app/bin export PYTHONPATH=$PYTHONPATH:~/app/lib/pythonX.Y/site-packages mkdir -p ~/app/bin ~/app/lib/pythonX.Y/site-packages python setup.py install --prefix=~/app --rgt-tool=hint
The above command will install the package to your ~/app folder. You can change the location of this folder to whichever you want. Note that in the above commands we made some modifications to your PYTHONPATH and PATH variables. The PYTHONPATH variable should contain all the paths to python libraries and the PATH variable should contain the paths to all binaries you want to execute.
Furthermore, we provide some extra options for RGT packages installation:
1. Data Path: RGT uses data such as the genome, genome size, default hidden Markov models, etc. All these data will be installed by default to ~/rgtdata. However you may want to modify such path by using this option.
WARNING: Some data types (such as the genome) are too big to be in our installation structure. Please download our full data package here and merge it with your installed rgtdata path.
Learn more about the RGT Data Folder.
2. RGT Tool: If this option is not used, all RGT tools will be installed. In order to install only HINT please use this as in the example below.
The example below shows an example of installation using all these options:
python setup.py install --prefix=~/app --rgt-data-path=~/app --rgt-tool=hint
We highly recommend you to install the latest version of HINT by pip. These archived versions are not supported anymore.
|1.1.1||Download||Correction in the histone-only HMM and minor bugs.|
|1.1.0||Download||Bug correction and inclusion of tag-count footprint score.|
|1.0.0||Download||Inclusion of bias correction (HINT-BC).|
|0.1.1||Download||First stable release of HINT.|