Please check the following instructions to complete your installation.
Python version must be >= 2.7.
Ribo-TISH can run on python3, but extensive tests are not performed yet.
| Pysam: | >= 0.8.3 |
|---|---|
| Scipy: | >= 0.15.1 |
| Matplotlib: | >= 1.4.3 |
Ribo-TISH cannot run on Windows because Pysam does not support Windows installation.
The easiest way to install Ribo-TISH is through PyPI system. Get pip if it's not available in your system.
Then under command line:
$ pip install ribotish
PyPI will install all dependents automatically if they are absent.
To upgrade Ribo-TISH, type:
$ pip install -U ribotish
If you do not want pip to fix dependencies, type:
$ pip install --no-deps ribotish
To install/upgrade Ribo-TISH under HOME directory without fixing dependencies:
$ pip install --no-deps -U --user ribotish
To install a source distribution, download source from PyPI or GitHub. The latest updates usually appear on GitHub first.:
$ git clone https://github.com/zhpn1024/ribotish
Go to the directory and simply run the install script:
$ python setup.py install
By default, the script will install python library and executable codes globally, which means you need to be root or administrator of the machine so as to complete the installation.
If I want to install everything under my own HOME directory, use this command:
$ python setup.py install --prefix /home/pzhang/
or:
$ python setup.py install --user
After running the setup script, you might need to add the install location to your PYTHONPATH and PATH environment variables. The process for doing this varies on each platform, but the general concept is the same across platforms.
To set up your PYTHONPATH environment variable, you may need to add the value PREFIX/lib/pythonX.Y/site-packages to your existing PYTHONPATH. In this value, X.Y stands for the major–minor version of Python you are using (such as 2.7). PREFIX is the install prefix where you installed ribotish. If you did not specify a prefix on the command line, it will be installed using Python's sys.prefix value.
On Linux, using bash, you can include the new value in PYTHONPATH by
adding this line to ~/.bashrc or ~/.bash_profile. For example:
$ export PYTHONPATH=~/lib/python2.7/site-packages:$PYTHONPATH
Just like your PYTHONPATH, you may also need to add a new value to your PATH environment variable so that you can use the ribotish command line directly. This time you need to add PREFIX/bin to your PATH environment variable. The process is the same as for the PYTHONPATH variable:
$ export PATH=~/bin:$PATH