From a19184646e60d68a17041a0292ed9433e07dda73 Mon Sep 17 00:00:00 2001
From: Dan Leehr <dan.leehr@duke.edu>
Date: Thu, 22 Aug 2019 15:31:19 -0400
Subject: [PATCH 1/3] Update Dockerfile to install python3 branches of
 predictors

- Removing separate LIBSVM installation (it is now available via pip)
- Removes python-pip (Python 2) installer, since we're entirely python 3
---
 Dockerfile | 29 +++++------------------------
 1 file changed, 5 insertions(+), 24 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 159ee8e..9e8dc46 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,9 @@
 FROM ubuntu:xenial
-MAINTAINER "Dan Leehr" dan.leehr@duke.edu
+LABEL maintainer="dan.leehr@duke.edu"
 
 RUN apt-get update && apt-get install -y \
   git \
-  python3 python3-pip python-pip\
+  python3 python3-pip\
   r-base
 
 ### Step 1: Install the worker and its dependencies
@@ -14,34 +14,15 @@ RUN pip3 install -r requirements.txt
 ADD . /opt/tf-predictions-worker/
 ENV PATH /opt/tf-predictions-worker/:$PATH
 
-### Step 2: Install LIBSVM, needed by predict-tf-binding
-# Makefile has no install target, so we compile and update PATH
-# Owned by root and placed in /opt
-
-ENV LIBSVM_VER 321
-RUN curl -SL https://github.com/cjlin1/libsvm/archive/v${LIBSVM_VER}.tar.gz | tar -xzC /opt # makes /opt/libsvm-321
-WORKDIR /opt/libsvm-${LIBSVM_VER}
-RUN make
-
-# Build shared lib for python bindings
-WORKDIR /opt/libsvm-${LIBSVM_VER}/python
-RUN make
-
-# Install libsvm and python bindings
-# These have no installer so we place the library and python bindings manually
-RUN cp /opt/libsvm-${LIBSVM_VER}/libsvm.so* /usr/lib/
-RUN ldconfig
-RUN cp /opt/libsvm-${LIBSVM_VER}/python/*.py /usr/local/lib/python2.7/dist-packages/
-
 ### Step 3: Install Predict-TF-Binding from GitHub
 WORKDIR /opt/
-RUN git clone https://github.com/Duke-GCB/Predict-TF-Binding.git predict-tf-binding
-RUN pip install -r /opt/predict-tf-binding/requirements.txt
+RUN git clone -b python3 https://github.com/Duke-GCB/Predict-TF-Binding.git predict-tf-binding
+RUN pip3 install -r /opt/predict-tf-binding/requirements.txt
 ENV PATH /opt/predict-tf-binding/:$PATH
 
 ### Step 4: Install Predict-TF-Preference from GitHub
 WORKDIR /opt/
-RUN git clone https://github.com/Duke-GCB/Predict-TF-Preference.git predict-tf-preference
+RUN git clone -b python3 https://github.com/Duke-GCB/Predict-TF-Preference.git predict-tf-preference
 ENV PATH /opt/predict-tf-preference/:$PATH
 
 # Switch to non-root user

From 1fcded3e508a62bc42a6b70b951a2537d96b608c Mon Sep 17 00:00:00 2001
From: Dan Leehr <dan.leehr@duke.edu>
Date: Thu, 22 Aug 2019 15:46:04 -0400
Subject: [PATCH 2/3] Switch to python 3.7 base

- libsvm was failing to install due to an ascii codec error in python 3.5, so I switched from ubuntu base image to python 3.7
---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 9e8dc46..f3b8ec3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,8 @@
-FROM ubuntu:xenial
+FROM python:3.7
 LABEL maintainer="dan.leehr@duke.edu"
 
 RUN apt-get update && apt-get install -y \
   git \
-  python3 python3-pip\
   r-base
 
 ### Step 1: Install the worker and its dependencies

From 1e1ce8787139d185c8c75a4fbf535516b47b1841 Mon Sep 17 00:00:00 2001
From: Dan Leehr <dan.leehr@duke.edu>
Date: Fri, 23 Aug 2019 09:41:09 -0400
Subject: [PATCH 3/3] Restore master branches for predict-tf-* repos

After merging https://github.com/Duke-GCB/Predict-TF-Binding/pull/46 and https://github.com/Duke-GCB/Predict-TF-Preference/pull/5
---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f3b8ec3..a6971d4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,13 +15,13 @@ ENV PATH /opt/tf-predictions-worker/:$PATH
 
 ### Step 3: Install Predict-TF-Binding from GitHub
 WORKDIR /opt/
-RUN git clone -b python3 https://github.com/Duke-GCB/Predict-TF-Binding.git predict-tf-binding
+RUN git clone https://github.com/Duke-GCB/Predict-TF-Binding.git predict-tf-binding
 RUN pip3 install -r /opt/predict-tf-binding/requirements.txt
 ENV PATH /opt/predict-tf-binding/:$PATH
 
 ### Step 4: Install Predict-TF-Preference from GitHub
 WORKDIR /opt/
-RUN git clone -b python3 https://github.com/Duke-GCB/Predict-TF-Preference.git predict-tf-preference
+RUN git clone https://github.com/Duke-GCB/Predict-TF-Preference.git predict-tf-preference
 ENV PATH /opt/predict-tf-preference/:$PATH
 
 # Switch to non-root user