Installation¶
Note: DeFCoM was developed in a Linux environment and tested for Linux and Mac operating systems. Though it should also work with the Windows operating system, we cannot guarantee its portability.
Please report any issues with installing DeFCoM or bugs in the code here.
Dependencies¶
DeFCoM is designed to run using Python 2.7 or later. To successfully install the DeFCoM software package, the following Python packages (with version requirements) must already be installed in your Python environment:
- NumPy >= 1.8 (Install Guide)
- SciPy >= 0.14 (Install Guide)
- Pysam >= 0.9 (Install Guide)
- Sci-kit Learn >= 0.18 (Install Guide)
Several of the packages can be installed easily using pip (installation instructions here). NumPy and SciPy should be installed before Sci-kit Learn. Be sure to check dependency requirements for these packages also.
Downloading¶
Major releases of the DeFCoM Python package can be downloaded via Bitbucket as a compressed (.zip) folder. If you have mercurial installed, the latest development version can be retrieved from the code repository using the command
hg clone https://bryancquach@bitbucket.org/bryancquach/defcom
To retrieve a specific branch named branch_name from the repository use
hg clone https://bryancquach@bitbucket.org/bryancquach/defcom -r branch_name
Installing¶
Using pip¶
If you have pip installed on your system, the latest official release of DeFCoM can be installed with the command-line call
pip install defcom or pip install defcom --user (user-only install)
From source¶
If retrieving a zipped version of the package, first unzip the contents. From
a command-line terminal, traverse one level into the unzipped package
directory (should be named defcom) where setup.py is located. You can
optionally test to see whether the install will be successful by using the
command
python setup.py test
Use the following command to run the installation:
python setup.py install
If you do not have administrative privileges then the user-specific install command is
python setup.py install --user