You can either download a specific version of NGSUtils or clone our Git repository. If you have
git installed on
your computer, this is the recommended method for installation.
Go to: https://github.com/ngsutils/ngsutils/tags to download the latest version of NGSUtils.
The easiest way to install (and get updates) is to checkout the code from GitHub directly. To do this, you’ll need to clone our repository.
$ git clone git://github.com/ngsutils/ngsutils.git
$ cd ngsutils
Once you have the code downloaded, you need to run
make in the ngsutils directory. This will create a virtualenv folder
(venv) and install the needed libraries. Once you run
make, you should be able to run the
gtfutils programs. It is often helpful to add these files to your $PATH so that you can call them
directly without entering their full pathnames.
If you need to use a custom python interpreter, such as
python2.6, then you can specify this at the command line before running
The given interpreter will be used to create the virtualenv environment and be used by NGSUtils in the future without needing to specify the
$ PYTHON=python2.6 make
Note: for RHEL5, it is recommended that you add the EPEL repository to your yum configuration and install the python26 packages. This will let NGSUtils use the proper version of Python without disrupting any system utilities.
Also, virtualenv is now bundled with NGSUtils to make installation easier.
Additionally, Cython requires that the Python headers be present on the system. For a linux system this can be achieved by installing ‘python-devel’ or similar.
Here are some other tools that NGSUtils will work with.
Some commands in NGSUtils require indexed BAM, FASTA, or BED files to work. These may all be indexed using samtools.