From 1f8d398faa7e749a0eccf897d71510713d5163b8 Mon Sep 17 00:00:00 2001
From: evanbiederstedt <evan.biederstedt@gmail.com>
Date: Tue, 4 Jun 2019 11:27:10 -0400
Subject: [PATCH 1/3] added a requirements.txt file for users

---
 neoantigen.py    | 3 ++-
 requirements.txt | 4 ++++
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 requirements.txt

diff --git a/neoantigen.py b/neoantigen.py
index bb26859..f179825 100644
--- a/neoantigen.py
+++ b/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
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..5503bf3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+psutil(>=5.6.2)
+python-dateutil(>=2.8.0)
+pandas(>=0.24.2)
+joblib(>=0.13.2)
\ No newline at end of file

From 0bb93146217fa5390d48c9fa09ab51028ca8d5bd Mon Sep 17 00:00:00 2001
From: evanbiederstedt <evan.biederstedt@gmail.com>
Date: Tue, 4 Jun 2019 11:31:29 -0400
Subject: [PATCH 2/3] revised the README

---
 README.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2536e56..7df6b3c 100644
--- a/README.md
+++ b/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. 
 ```

From 3111c659dcb2b95ad8b75b0d8ff2a04e4cb49abc Mon Sep 17 00:00:00 2001
From: evanbiederstedt <evan.biederstedt@gmail.com>
Date: Thu, 6 Jun 2019 11:22:13 -0400
Subject: [PATCH 3/3] added travis config

---
 .travis.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..0d381cb
--- /dev/null
+++ b/.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