Merge pull request #100 from Illumina/public_push

Merge content from internal repo for release
Illumina · Oct 11, 2019 · 46ee23c · 46ee23c
2 parents 6720142 + f0666f9
commit 46ee23c
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -84,8 +84,11 @@ set(HAPLOTYPES_ALL_LIBS ${HAPLOTYPES_LIBRARY}
                         ${CMAKE_THREAD_LIBS_INIT})
 
 
-include(GetGitRevisionDescription)
-git_describe(HAPLOTYPES_VERSION)
+execute_process(COMMAND git describe --tags --always
+    OUTPUT_VARIABLE HAPLOTYPES_VERSION
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+)
 
 configure_file("${CMAKE_CURRENT_SOURCE_DIR}/src/c++/include/Version.hh.in"
                "${CMAKE_BINARY_DIR}/include/Version.hh")

diff --git a/Dockerfile b/Dockerfile
@@ -1,31 +1,36 @@
 FROM ubuntu:18.04
 
 ENV DEBIAN_FRONTEND=noninteractive
-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 -y
-RUN apt-get clean -y
 
-RUN pip install bx-python
+RUN apt-get update && \
+    apt-get install -y \
+        autoconf \
+        build-essential \
+        bzip2 \
+        cmake \
+        cython \
+        git \
+        libbz2-dev \
+        libncurses5-dev \
+        openjdk-8-jdk \
+        pkg-config \                    
+        python \
+        python2.7 \
+        python2.7-dev \                    
+        python-setuptools \
+        python-pip \
+        python-psutil \                    
+        python-numpy \
+        python-pandas \
+        python-distribute \
+        python-pysam \
+        python-scipy \                    
+        software-properties-common \
+        wget \
+        zlib1g-dev && \
+    apt-get clean -y
 
-RUN echo oracle-java11-installer shared/accepted-oracle-license-v1-2 select true | debconf-set-selections && \
-    add-apt-repository -y ppa:linuxuprising/java && \
-    apt-get update && \
-    apt-get install -y oracle-java11-installer && \
-    rm -rf /var/lib/apt/lists/* && \
-    rm -rf /var/cache/oracle-jdk11-installer
+RUN pip install bx-python
 
 # copy git repository into the image
 RUN mkdir -p /opt/hap.py-source

diff --git a/Dockerfile.centos6 b/Dockerfile.centos6
@@ -4,30 +4,43 @@ ENV HOME /root
 ENV LANG en_US.UTF-8
 ENV LC_ALL en_US.UTF-8
 
-RUN  yum install -y wget curl tar gzip bzip2 which perl
-
-RUN  mkdir -p /opt/illumina/haplocompare && \
+RUN yum install -y \
+    bzip2 \
+    bzip2-devel \
+    centos-release-scl \
+    cmake \
+    curl \
+    devtoolset-8-gcc \
+    devtoolset-3-binutils \
+    devtoolset-8-gcc-c++ \
+    devtoolset-8-gcc-gfortran \
+    git \
+    gzip \
+    java-1.8.0-openjdk \
+    ncurses-devel \ 
+    perl \
+    tar \
+    wget \
+    which \
+    zlib-devel \
+
+RUN yum upgrade -y && yum update -y && yum clean all
+
+RUN mkdir -p /opt/illumina/haplocompare && \
      cd /opt/illumina/haplocompare && \
      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
      bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
 
 ENV PATH /opt/miniconda2/bin:${PATH}
 
-RUN  yum install -y centos-release-scl && \
-     yum install -y devtoolset-3-gcc devtoolset-3-binutils && \
-     yum install -y devtoolset-3-gcc-c++ devtoolset-3-gcc-gfortran && \
-     yum install -y cmake bzip2-devel ncurses-devel zlib-devel git
-
-RUN  conda config --add channels bioconda && \
-     conda install -y cython numpy scipy biopython matplotlib pandas pysam bx-python pyvcf cyvcf2 nose
-
-RUN yum upgrade -y && yum update -y && yum clean all
+RUN conda config --add channels bioconda && \
+    conda install -y cython numpy scipy biopython matplotlib pandas pysam bx-python pyvcf cyvcf2 nose
 
 COPY . /opt/illumina/haplocompare/hap.py-source
 WORKDIR /opt/illumina/haplocompare/hap.py-source
 
 # patch samtools for centos 6
-RUN  cd external && \
+RUN cd external && \
      tar xvzf samtools.tar.gz && \
      cd samtools && \
      cat Makefile | sed 's/-ldl/-ldl -ltinfo/' > Makefile.bak && \
@@ -36,12 +49,6 @@ RUN  cd external && \
      rm -f samtools.tar.gz && \
      tar czvf samtools.tar.gz samtools
 
-
-ENV JDK_VERSION 8u11
-ENV JDK_BUILD_VERSION b12
-RUN curl -LO "http://download.oracle.com/otn-pub/java/jdk/$JDK_VERSION-$JDK_BUILD_VERSION/jdk-$JDK_VERSION-linux-x64.rpm" -H 'Cookie: oraclelicense=accept-securebackup-cookie' && rpm -i jdk-$JDK_VERSION-linux-x64.rpm && rm -f jdk-$JDK_VERSION-linux-x64.rpm && yum clean all
-ENV JAVA_HOME /usr/java/default
-
 # get + install ant
 WORKDIR /opt
 RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && \

diff --git a/Dockerfile.ubuntu-with-tests b/Dockerfile.ubuntu-with-tests
@@ -1,31 +1,36 @@
 FROM ubuntu:18.04
 
 ENV DEBIAN_FRONTEND=noninteractive
-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 -y
-RUN apt-get clean -y
 
-RUN pip install bx-python
+RUN apt-get update && \
+    apt-get install -y \
+        autoconf \
+        build-essential \
+        bzip2 \
+        cmake \
+        cython \
+        git \
+        libbz2-dev \
+        libncurses5-dev \
+        openjdk-8-jdk \
+        pkg-config \                    
+        python \
+        python2.7 \
+        python2.7-dev \                    
+        python-setuptools \
+        python-pip \
+        python-psutil \                    
+        python-numpy \
+        python-pandas \
+        python-distribute \
+        python-pysam \
+        python-scipy \                    
+        software-properties-common \
+        wget \
+        zlib1g-dev && \
+    apt-get clean -y
 
-RUN echo oracle-java11-installer shared/accepted-oracle-license-v1-2 select true | debconf-set-selections && \
-    add-apt-repository -y ppa:linuxuprising/java && \
-    apt-get update && \
-    apt-get install -y oracle-java11-installer && \
-    rm -rf /var/lib/apt/lists/* && \
-    rm -rf /var/cache/oracle-jdk11-installer
+RUN pip install bx-python
 
 # copy git repository into the image
 RUN mkdir -p /opt/hap.py-source

diff --git a/RELEASES.md b/RELEASES.md
@@ -1,5 +1,27 @@
 # Hap.py Release Notes / Change Log
 
+## v0.3.12
+
+| Ticket  | Description                                                                        |
+|---------|------------------------------------------------------------------------------------|
+| HAP-355 | Ensure compatibility with genome VCF from DRAGEN pipelines                         |
+| HAP-356 | quantify module throws regex error                                                 |
+| HAP-357 | Deal with change in Java license terms                                             |
+| HAP-359 | Hap.py crashes when ingesting variants genotyped as <NON_REF>                      |
+| HAP-360 | Apply non-ref filter to truth set when --preprocess-truth is set                   |
+| HAP-361 | Hap.py "blocksplit" processes still failing on DRAGEN gVCFs even with pre-filtering NON_REF genotypes 
+| HAP-362 | Hap.py blocksplit sometimes crashes with "invalid next size (fast)" error          |
+| HAP-363 | Use 'git describe' to obtain version number during Cmake                           |
+
+## v0.3.11
+
+| Ticket  | Description                                                                        |
+|---------|------------------------------------------------------------------------------------|
+| HAP-341 | Update rtgtools to 3.10.1                                                          |
+| HAP-342 | som.py output tables to quantify / GA4GH format                                    |
+| HAP-346 | src/sh/illumina-setup.sh out of date                                               |
+| HAP-352 | string formatting in som.py: last interval is always [1.0, 1.0] in *extended.csv   |
+
 ## v0.3.10
 
 | Ticket  | Description                                                                        |