Installing SIDR¶
SIDR can be installed either using pip–the python package manager–or manually using the included setup.py file.
Dependencies¶
SIDR is able to install all of its dependencies from PyPI automatically. This should work in most cases. If you are installing under Python 3, you may need to manually install Cython with:
pip install cython
If you have a locally installed version of HTSLib, you can include it by using the commands:
export HTSLIB_LIBRARY_DIR=/usr/local/lib
export HTSLIB_INCLUDE_DIR=/usr/local/include
before installing SIDR.
OSX¶
Users running a recent version of OSX may need to install an alternative python distribution like that provided by Homebrew. If SIDR installation fails with permission errors, this is the most likely solution.
Using a Virtualenv¶
Some cluster users may need to setup a Python virtualenv due to the nature of working with a cluster environment. A virtualenv can be setup with the commands:
virtualenv venv
. venv/bin/activate
If necessary, virtualenv can be installed in the user’s home directory (~/.local/bin must be in $PATH) with the following command:
pip install --user virtualenv
Installing from PyPI¶
Installing from PyPI is the easiest method, and thus the recommended one. To install SIDR:
pip install sidr
Installing from Source with pip¶
Note
When installing from source, setuptools will attempt to contact PyPI to install dependencies. If this is not an option then dependencies will need to be manually installed.
If PyPI is not an option or if you’d like to run the latest development version, SIDR can be installed by running the following command:
pip install git+https://github.com/damurdock/SIDR.git
If you’re installing SIDR in order to develop it, download the source from GitHub and install it by running the following command in the unzipped source directory:
pip install --editable .