From 597a8a62352a65fe359a260106901c44c61c80d8 Mon Sep 17 00:00:00 2001
From: akmorrow13 <hadoop@ip-172-31-40-31.us-west-2.compute.internal>
Date: Mon, 19 Nov 2018 03:41:34 +0000
Subject: [PATCH 1/3] updated Mango for Spark 2.3.2

---
 mango/runtime/Dockerfile          | 17 +++++++++++++----
 mango/test.py                     |  2 +-
 spark-and-maven/build/download.sh |  2 +-
 3 files changed, 15 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 spark-and-maven/build/download.sh

diff --git a/mango/runtime/Dockerfile b/mango/runtime/Dockerfile
index af8acc6..86891d3 100644
--- a/mango/runtime/Dockerfile
+++ b/mango/runtime/Dockerfile
@@ -20,24 +20,33 @@ ENV PYSPARK_SUBMIT_ARGS "--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-p
 ENV PYTHONPATH ${SPARK_HOME}/python:${SPARK_HOME}/python/lib/py4j-0.10.4-src.zip
 
 #environment variables PYSPARK_PYTHON and PYSPARK_DRIVER_PYTHON
-ENV PYSPARK_PYTHON /usr/bin/python
-ENV  PYSPARK_DRIVER_PYTHON /usr/bin/python
-
+ENV PYSPARK_PYTHON /usr/bin/python3
 
 # Install make and pip/python dependencies
 RUN apt-get update && apt-get install -y \
   git \
   make \
-  python-pip \
+  python3-pip \
   npm \
   nodejs \
   python-tk
 
+# alias python to python3.6
+RUN alias pip=pip3
+RUN alias python=python3
+RUN echo '#!/bin/bash\npython3 "$@"' > /usr/bin/python && \
+    chmod +x /usr/bin/python
+
+RUN echo '#!/bin/bash\npip3 "$@"' > /usr/bin/pip && \
+    chmod +x /usr/bin/pip
+
+RUN pip
 RUN ln -s /usr/bin/nodejs /usr/bin/node
 
 # set permissions for running npm. Required for mango-viz
 RUN npm config set bdgenomics.mango.pileup:unsafe-perm
 
+
 # prepare mango-viz and mango-python
 WORKDIR /opt/cgl-docker-lib/mango/mango-python
 RUN make prepare && make develop
diff --git a/mango/test.py b/mango/test.py
index 2eb13f2..eeadaea 100644
--- a/mango/test.py
+++ b/mango/test.py
@@ -9,7 +9,7 @@ class TestMango(unittest.TestCase):
 
     def test_docker_call_browser(self):
         out, err = check_docker_output(tool='quay.io/ucsc_cgl/mango')
-        self.assertTrue('Using SPARK_SUBMIT=' in out)
+        self.assertTrue('Using spark-submit=' in out)
         self.assertTrue('Argument "reference" is required' in out)
 
     def test_docker_call_notebook(self):
diff --git a/spark-and-maven/build/download.sh b/spark-and-maven/build/download.sh
old mode 100644
new mode 100755
index f1cc2da..ea61773
--- a/spark-and-maven/build/download.sh
+++ b/spark-and-maven/build/download.sh
@@ -7,7 +7,7 @@ mirror=$(python -c "from urllib2 import urlopen; import json; print json.load( u
 
 # pull down spark
 mkdir /opt/apache-spark
-curl ${mirror}spark/spark-2.1.2/spark-2.1.2-bin-hadoop2.6.tgz \
+curl ${mirror}spark/spark-2.3.2/spark-2.3.2-bin-hadoop2.7.tgz \
   | tar --strip-components=1 -xzC /opt/apache-spark
 
 # we rely on apache maven > 3.1.1 to build ADAM, so we can't use the

From 5638e300bf6a42afe58cc84c30f77138df5d7d23 Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Tue, 27 Nov 2018 11:52:36 -0800
Subject: [PATCH 2/3] bump cannoli to recent branch

---
 cannoli/build/Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/cannoli/build/Dockerfile b/cannoli/build/Dockerfile
index ff099f7..f90854c 100644
--- a/cannoli/build/Dockerfile
+++ b/cannoli/build/Dockerfile
@@ -9,8 +9,6 @@ RUN git clone https://github.com/bigdatagenomics/cannoli.git
 
 # build cannoli
 WORKDIR /home/cannoli
-RUN git checkout 122ead2219b987bb60e5f108a2d261e056abc86e
-RUN ./scripts/move_to_spark_2.sh
-RUN ./scripts/move_to_scala_2.11.sh
+RUN git checkout 4395e5b2e6040cbe5a24398d87ae49535fa62a23
 
 RUN /opt/apache-maven-3.3.9/bin/mvn package -DskipTests

From e18ed932dfa7c1bc173e30772efb8700139f0fab Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Thu, 29 Nov 2018 16:22:55 -0800
Subject: [PATCH 3/3] updated avocado by removing spark scripts

---
 avocado/build/Dockerfile | 2 --
 1 file changed, 2 deletions(-)

diff --git a/avocado/build/Dockerfile b/avocado/build/Dockerfile
index 7b4653a..4ffdfff 100644
--- a/avocado/build/Dockerfile
+++ b/avocado/build/Dockerfile
@@ -9,7 +9,5 @@ RUN git clone https://github.com/bigdatagenomics/avocado.git
 
 # build avocado
 WORKDIR /home/avocado
-RUN ./scripts/move_to_spark_2.sh
-RUN ./scripts/move_to_scala_2.11.sh
 
 RUN /opt/apache-maven-3.3.9/bin/mvn package -DskipTests