Installation

Fundamental dependencies

  • python 2.7
  • samtools >= 0.1.18
  • R >= 3.0

Setting up virtualenv

Create and activate a python virtual environment using virtualenv. Detailed instructions here.

If pip is installed, virtualenv can be installed using pip:

$ pip install virtualenv
$ virtualenv smalr_venv
$ . smalr_venv/bin/activate

If pip is NOT installed:

$ curl -O https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.0.1.tar.gz
$ tar xvfz virtualenv-13.0.1.tar.gz
$ cd virtualenv-13.0.1
$ python virtualenv.py smalr_venv
$ . smalr_venv/bin/activate

NOTE: This virtual environment must be activated to install & run SMALR

Installing mBin

With the virtual environment activated, clone SMALR source code from GitHub to a local SMALR repository:

$ git clone https://github.com/fanglab/SMALR.git

Install SMALR and required packages inside your virtual environment:

$ cd SMALR
$ python setup.py install

Confirm successful installation by testing both SMsn and SMp protocols:

$ cd test
$ ./run_test_SMsn.sh

This should generate the contig-specific folder J99_SMsn, containing pipeline output.

$ ./run_test_SMp.sh

This should generate the contig-specific folders scf7180000000008|quiver_SMp, scf7180000000009|quiver_SMp, scf7180000000010|quiver_SMp, and scf7180000000011|quiver_SMp, each containing pipeline output.