From b678d1456f368ffba2be55745d6dd76e543cb2ac Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Fri, 10 Jun 2016 20:33:26 -0400
Subject: [PATCH 1/3] Update Ubuntu dependencies for matplotlib-2.0.0b1 #84

- libfreetype6-dev satisfies the freetype requirement.

- pkg-config addresses freetype detection by matplotlib (see
  matplotlib/matplotlib#3029).
---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 6f9ebe0..71a8273 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,7 +19,7 @@ RUN echo 'deb http://cran.rstudio.com/bin/linux/ubuntu trusty/' >> /etc/apt/sour
 RUN apt-get update
 
 # Install dependencies
-RUN apt-get -y install git python-tables python-setuptools python-pip python-dev cython libhdf5-serial-dev r-base python-rpy2
+RUN apt-get -y install git python-tables python-setuptools python-pip python-dev cython libhdf5-serial-dev r-base python-rpy2 libfreetype6-dev pkg-config
 
 # Upgrade numexpr
 RUN pip install numexpr --upgrade

From 0878bb366379469d57655229a19e68a5312535e0 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Fri, 10 Jun 2016 20:36:48 -0400
Subject: [PATCH 2/3] Fix cython NoneType errors in #84

setup.py chokes when installing more than 1 cython module.  In the
current requirements.txt pandas, scipy, and h5py all use cython during
compilation.  As a workaround, pre-install these using pip.
---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 71a8273..49504e2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -29,7 +29,9 @@ RUN Rscript -e 'options("repos" = c(CRAN = "http://cran.rstudio.com/")); install
 
 # Install poretools
 RUN git clone https://github.com/arq5x/poretools /tmp/poretools
-RUN cd /tmp/poretools && python setup.py install
+WORKDIR /tmp/poretools
+RUN pip install -r requirements.txt
+RUN python setup.py install
 
 ############## INSTALLATION END ##############
 

From 475a8b79b64365a09ad632e915d8096aad6d2201 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Fri, 10 Jun 2016 21:53:46 -0400
Subject: [PATCH 3/3] Fix NumPy ABI compatibility runtime error for #84

---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 49504e2..c57e9a0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,6 +21,8 @@ RUN apt-get update
 # Install dependencies
 RUN apt-get -y install git python-tables python-setuptools python-pip python-dev cython libhdf5-serial-dev r-base python-rpy2 libfreetype6-dev pkg-config
 
+# Upgrade numpy
+RUN easy_install --upgrade numpy
 # Upgrade numexpr
 RUN pip install numexpr --upgrade