Merge pull request #1 from taylor-lab/develop

Added requirements.txt for python libraries

.travis.yml

@@ -0,0 +1,11 @@
+language: python
+python:
+    - 2.7
+install:
+    - sudo apt-get -y update
+    - pip install codecov
+    - pip install -r requirements.txt
+script:
+    - nosetests
+after_success:
+    - codecov

README.md

@@ -12,11 +12,16 @@ The pipeline has four main steps:
 
 
 ## Install
-Clone the repo and you are ready to go:
+
+Clone the repo and install any necessary python2 libraries from `requirements.txt`. Note that this repo is currently only compatible with Python 2.7, not Python 3.x :
+
 ```bash
 git clone https://github.com/taylor-lab/neoantigen-dev.git
+cd neoantigen-dev
+pip install -r requirements.txt
 ```
 
+
 ## Usage
 NOTE: For POLYSOLVER step, the pipeline requires 8 cores. 
 ```

neoantigen.py

@@ -1,4 +1,5 @@
-#!/opt/common/CentOS_6-dev/python/python-2.7.10/bin/python
+#!/usr/bin/env python2
+
 import os, sys, subprocess, psutil
 import argparse, re, errno
 import time, datetime, dateutil.parser

requirements.txt

@@ -0,0 +1,4 @@
+psutil(>=5.6.2)
+python-dateutil(>=2.8.0)
+pandas(>=0.24.2)
+joblib(>=0.13.2)