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 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 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