Merge pull request #73 from Bioinformatics/HAP-318

HAP-318 and HAP-319
Illumina · Jun 3, 2017 · d9a9967 · d9a9967
2 parents 8faf71c + 0f5fe57
commit d9a9967
Show file tree

Hide file tree

Showing 5 changed files with 91 additions and 67 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,52 +1,23 @@
-FROM ubuntu:14.04
-
-RUN apt-get update
-RUN apt-get upgrade -y
-
-# install python and PIP
-RUN apt-get install python2.7 python2.7-dev -y
-RUN apt-get install cython -y
-RUN apt-get install python-setuptools -y
-RUN apt-get install python-pip -y
-RUN apt-get install python-numpy -y
-RUN apt-get install zlib1g-dev -y
-# ideally, we don't want to use the ubuntu version
-# here because this bloats the Docker image
-# RUN apt-get install python-pandas -y
-RUN easy_install -U distribute
-
-# numpy and such
-RUN apt-get install build-essential -y
-RUN apt-get install gfortran -y
-RUN apt-get install -y libatlas-base-dev
-RUN apt-get install pkg-config -y
+FROM ubuntu:16.04
+
+RUN apt-get update && apt-get upgrade -y
+RUN apt-get install build-essential zlib1g-dev libbz2-dev pkg-config cmake libncurses5-dev autoconf -y
+RUN apt-get install git bzip2 wget -y
+RUN apt-get install python2.7 python2.7-dev python \
+                    python-setuptools \
+                    python-pip \
+                    python-psutil \
+                    cython \
+                    python-numpy \
+                    python-pandas \
+                    python-distribute \
+                    python-pysam \
+                    python-scipy \
+                    -y
 RUN apt-get install software-properties-common python-software-properties -y
-RUN apt-get install cmake -y
-
-# hap.py v0.3.7+ requires g++ 4.9
-RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y
-RUN apt-get update
-RUN apt-get install g++-4.9 -y
-RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50
-RUN update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50
+RUN apt-get clean -y
 
-# upgrade to newest versions / install
-RUN pip install --upgrade cython
-RUN pip install --upgrade numpy
-RUN pip install --upgrade pandas
-RUN pip install pybedtools
-RUN pip install pysam
 RUN pip install bx-python
-RUN pip install scipy
-
-# boost and cmake for hap.py
-RUN apt-get install libncurses5-dev -y
-RUN apt-get install git -y
-RUN apt-get install samtools -y
-RUN apt-get install bzip2 -y
-RUN apt-get install wget -y
-RUN apt-get install libbz2-dev -y
-
 
 RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
     add-apt-repository -y ppa:webupd8team/java && \
@@ -55,8 +26,6 @@ RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true
     rm -rf /var/lib/apt/lists/* && \
     rm -rf /var/cache/oracle-jdk8-installer
 
-RUN apt-get clean -y
-
 # copy git repository into the image
 RUN mkdir -p /opt/hap.py-source
 COPY . /opt/hap.py-source/
@@ -67,29 +36,22 @@ RUN mkdir -p /opt/hap.py-data
 # download HG19 reference data
 WORKDIR /opt/hap.py-data
 
-# This downloads from UCSC
-RUN /opt/hap.py-source/src/sh/make_hg19.sh
-
-# this downloads our copy from box.com (once available)
-# RUN wget https://illumina.app.box.com/s/1vwpu1w23p2qupukjjlrenq81mrtth1z/hg19.fa.bz2 -O /opt/hap.py-source/src/data/hg19.fa.bz2
-# RUN bzcat /opt/hap.py-source/src/data/hg19.fa.bz2 > /opt/hap.py-data/hg19.fa
-RUN samtools faidx /opt/hap.py-data/hg19.fa
-
 # get + install ant
 WORKDIR /opt
 RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && \
     tar xzf apache-ant-1.9.7-bin.tar.gz && \
     rm apache-ant-1.9.7-bin.tar.gz
 ENV PATH $PATH:/opt/apache-ant-1.9.7/bin
 
-# run hap.py installer in the image
+# run hap.py installer in the image, don't run tests since we don't have a reference file
 WORKDIR /opt/hap.py-source
-RUN HG19=/opt/hap.py-data/hg19.fa python install.py /opt/hap.py --with-rtgtools
+RUN python install.py /opt/hap.py --with-rtgtools --no-tests
+WORKDIR /opt/hap.py
+
+# run basic tests
+RUN bin/test_haplotypes
+
+# remove source folder
 WORKDIR /
 RUN rm -rf /opt/hap.py-source
 
-# Optionally set up I/O folders
-# RUN mkdir /data && chgrp users /data && chmod a+rwx /data
-# VOLUME /data
-# RUN useradd happy -m -s /bin/bash -G users
-# USER happy
diff --git a/Dockerfile.ubuntu-with-tests b/Dockerfile.ubuntu-with-tests
@@ -0,0 +1,59 @@
+FROM ubuntu:16.04
+
+RUN apt-get update && apt-get upgrade -y
+RUN apt-get install build-essential zlib1g-dev libbz2-dev pkg-config cmake libncurses5-dev autoconf -y
+RUN apt-get install git bzip2 wget -y
+RUN apt-get install python2.7 python2.7-dev python \
+                    python-setuptools \
+                    python-pip \
+                    python-psutil \
+                    cython \
+                    python-numpy \
+                    python-pandas \
+                    python-distribute \
+                    python-pysam \
+                    python-scipy \
+                    -y
+RUN apt-get install software-properties-common python-software-properties -y
+RUN apt-get clean -y
+
+RUN pip install bx-python
+
+RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
+    add-apt-repository -y ppa:webupd8team/java && \
+    apt-get update && \
+    apt-get install -y oracle-java8-installer && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm -rf /var/cache/oracle-jdk8-installer
+
+# copy git repository into the image
+RUN mkdir -p /opt/hap.py-source
+COPY . /opt/hap.py-source/
+
+# make minimal HG19 reference sequence
+RUN mkdir -p /opt/hap.py-data
+
+# get + install ant
+WORKDIR /opt
+RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && \
+    tar xzf apache-ant-1.9.7-bin.tar.gz && \
+    rm apache-ant-1.9.7-bin.tar.gz
+ENV PATH $PATH:/opt/apache-ant-1.9.7/bin
+
+# run hap.py installer in the image, don't run tests since we don't have a reference file
+WORKDIR /opt/hap.py-source
+RUN python install.py /opt/hap.py --with-rtgtools --no-tests
+
+# download HG19 reference data
+# This downloads from UCSC
+WORKDIR /opt/hap.py-data
+ENV PATH $PATH:/opt/hap.py/bin
+RUN /opt/hap.py-source/src/sh/make_hg19.sh && samtools faidx /opt/hap.py-data/hg19.fa
+# Run tests
+ENV HG19 /opt/hap.py-data/hg19.fa
+WORKDIR /opt/hap.py
+RUN /opt/hap.py-source/src/sh/run_tests.sh
+
+# remove source folder
+WORKDIR /
+RUN rm -rf /opt/hap.py-source
diff --git a/RELEASES.md b/RELEASES.md
@@ -5,6 +5,8 @@
 | Ticket  | Description                                                                        |
 |---------|------------------------------------------------------------------------------------|
 | HAP-317 | Update htslib to 1.4.1 and always check for BCF conversion errors                  |
+| HAP-318 | Update rtgtools to 3.8.1                                                           |
+| HAP-319 | Slimmer docker image without hg19 reference                                        |
 
 ## v0.3.8
 

diff --git a/external/make_dependencies.sh b/external/make_dependencies.sh
@@ -115,9 +115,9 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
         cd ${TLD}
         mkdir -p ${TLD}/rtg-tools
         cd rtg-tools
-        wget http://github.com/RealTimeGenomics/rtg-tools/archive/3.7.1.tar.gz -O ${TLD}/rtg-tools/rtg-tools.tar.gz
+        wget http://github.com/RealTimeGenomics/rtg-tools/archive/3.8.1.tar.gz -O ${TLD}/rtg-tools/rtg-tools.tar.gz
         tar xvf rtg-tools.tar.gz
-        cd rtg-tools-3.7.1
+        cd rtg-tools-3.8.1
 
         if [[ ! -z ${ANT_HOME} ]]; then
             $ANT_HOME/bin/ant zip-nojre
@@ -126,7 +126,7 @@ if [[ ! -z $BUILD_VCFEVAL ]]; then
         fi
         cd ..
 
-        RTG_ZIPFILE=$(ls rtg-tools-3.7.1/dist/*-nojre.zip | head -1)
+        RTG_ZIPFILE=$(ls rtg-tools-3.8.1/dist/*-nojre.zip | head -1)
         RTG_BASE=$(basename $RTG_ZIPFILE -nojre.zip)
         jar xvf $RTG_ZIPFILE
         mv $RTG_BASE ${ISD}/libexec/rtg-tools-install

diff --git a/happy.requirements.txt b/happy.requirements.txt
@@ -1,7 +1,8 @@
 Cython
 numpy
 pandas
-pybedtools
+psutil
+pip
 pysam
 nose
 scipy