massprf-pipeline

pipeline for genome wide MASSPRF analysis

Installation

Note: These instructions are by no means exhaustive and will change based on your individual shell configurations and environment. In general, this instruction (and the pipeline itself) assumes a unix environment running bash. Advanced users w/ different configurations should be able to install without these instructions.

0) Install massprf and massprf_preprocess. You can clone this repository and read within for build instructions. https://github.com/Townsend-Lab-Yale/MASSPRF

It is important to note that you may need to build both massprf and massprf_preprocess independently. The final executable for massprf will be in ./bin, while the massprf_preprocess executable will be in ./MASSPRF_preprocessing_08July2016.

0.1) Build symlinks to massprf and massprf_preprocess

Get the absolute path of your compiled massprf & MASSPRF_preprocess. These will be something like:

~/PATH/TO/MASSPRF/MASSPRF_10July2016/bin/massprf ~/PATH/TO/MASSPRF/MASSPRF_10July2016/MASSPRF_preprocessing_08July2016/MASSPRF_preprocess

Create a custom symlinks folder in your home directory if you haven't already. mkdir ~/symbolics

change to that directory:

cd ~/symbolics

Create links to massprf & massprf_preprocess in that directory

ln -s ~/PATH/TO/MASSPRF/MASSPRF_10July2016/bin/massprf massprf

ln -s ~/PATH/TO/MASSPRF/MASSPRF_10July2016/MASSPRF_preprocessing_08July2016/MASSPRF_preprocess massprf_preprocess

Add the symbolic link folder to your $PATH in ~/.bash_profile

vim ~/.bash_profile

Scroll to the line that says something like

PATH=$PATH:OTHERPATHS

Append a colon and add the path to your symbolic links, such that it looks like this:

PATH=$PATH:OTHERPATHS:$HOME/symbolics

1) Install conda package manager:

pip install conda

If you are working on a cluster, you may need to install miniconda directly from the package due to file permissioning/pip being unavailable. In this case, download the file from https://conda.io/miniconda.html , run it on the cluster, and make sure that the installation directory is added to your path via ~/.bashrc. After installing miniconda, use source ~/.bashrc to source the path, then type python and check that your python version is >3.5 and is produced by 'Continuum Analytics'

2) Make sure your conda is up to date by running:

conda update conda

3) Update python to 3.5, or (optionally) create a python 3.5 virtual environment:

conda update python

4) Get package dependencies

Add Bioconda channel to Conda:

conda config --add channels bioconda

Pandas:

conda install pandas

Biopython:

conda install biopython

Gffutils:

conda install gffutils

pyvcf:

conda install pyvcf

5) Clone this repository

git clone https://github.com/Townsend-Lab-Yale/massprf-pipeline.git

Usage:

To run example, see jobs.list