Merge branch 'release/0.7.0'

Author: Daniel Cooke

.dockerignore

@@ -0,0 +1,33 @@
+**/.classpath
+**/.dockerignore
+**/.env
+**/.git
+**/.gitignore
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/azds.yaml
+**/bin
+**/charts
+**/docker-compose*
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml
+**/.travis.yml
+README.md
+CONTRIBUTING.md
+logo.png
+**/doc
+**/cmake-build-debug
+**/test
+**/resources/forests/*
+**/build/*
+!**/build/cmake

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,16 +7,26 @@ about: Create a report to help us improve
 **Describe the bug**
 A clear and concise description of what the bug is.
 
+**Version**
+
+```shell
+$ octopus --version
+// PASTE OUTPUT HERE
+```
+
 **Command**
+Command line to install octopus:
+```shell
+$ 
+```
+
 Command line to run octopus:
 ```shell
 $ octopus
 ```
 
-**Desktop (please complete the following information):**
- - OS: [e.g. OSX High Sierra]
- - Version [e.g. v0.3.3-alpha]
- - Reference [e.g. hg19]
-
 **Additional context**
-Add any other context about the problem here.
+Add any other context about the problem here, e.g.
+
+ - Reference [e.g. hg19]. Please provide link to fasta if atypical.
+ - BAM files (if possible).

.gitignore

@@ -245,3 +245,13 @@ TSWLatexianTemp*
 .DS_Store
 .idea/
 cmake-build-debug/*
+
+# vccode
+.vscode/
+
+# Ninja
+build/rules.ninja
+build/.ninja_deps
+build/.ninja_log
+build/build.ninja
+build/compile_commands.json

CMakeLists.txt

@@ -7,28 +7,33 @@ include(CheckIPOSupported)
 project(octopus)
 
 set(octopus_VERSION_MAJOR 0)
-set(octopus_VERSION_MINOR 6)
-set(octopus_VERSION_PATCH 3)
-set(octopus_VERSION_RELEASE beta)
+set(octopus_VERSION_MINOR 7)
+set(octopus_VERSION_PATCH 0)
+set(octopus_VERSION_RELEASE "")
+
+# Generate list of compile commands.  This helps debugging and doesn't have a downside.
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+# Avoid warnings when using GMP_ROOT
+cmake_policy(SET CMP0074 NEW)
 
 # Get the current working branch
 execute_process(
     COMMAND git rev-parse --abbrev-ref HEAD
     WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-    OUTPUT_VARIABLE GIT_BRANCH
+    OUTPUT_VARIABLE GIT_BRANCH_
     OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 
 # Get the latest abbreviated commit hash of the working branch
 execute_process(
     COMMAND git log -1 --format=%h
     WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-    OUTPUT_VARIABLE GIT_COMMIT_HASH
+    OUTPUT_VARIABLE GIT_COMMIT_HASH_
     OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 
-add_definitions(-DGIT_COMMIT_HASH="${GIT_COMMIT_HASH}")
-add_definitions(-DGIT_BRANCH="${GIT_BRANCH}")
+set(GIT_BRANCH "${GIT_BRANCH_}")
+set(GIT_COMMIT_HASH "${GIT_COMMIT_HASH_}")
 
 configure_file (
     "${PROJECT_SOURCE_DIR}/src/config/version.h.in"
@@ -52,6 +57,10 @@ elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "3.8")
         message(FATAL_ERROR "Clang version must be at least 3.8!")
     endif()
+elseif(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "3.8")
+        message(FATAL_ERROR "Intel version must be at least 19.0!")
+    endif()
 else()
     message(WARNING "You are using an unsupported compiler! Compilation has only been tested with Clang and GCC.")
 endif()

Dockerfile

@@ -1,64 +1,23 @@
 FROM ubuntu:latest
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 # Get all apt dependencies
 RUN apt-get -y update
 RUN apt-get -y install software-properties-common
 RUN apt-get install -y --no-install-recommends apt-utils
 RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test
 RUN apt-get -y install \
-    gcc-8 g++-8 \
+    gcc g++ \
     build-essential \
-    make \
-    wget \
-    autotools-dev \
-    libicu-dev \
     git \
     curl \
-    libcurl4-openssl-dev \
-    pkg-config \
-    autoconf \
-    libbz2-dev \
-    liblzma-dev \
-    zlib1g-dev \
-    openssl \
-    libssl-dev \
-    libcrypto++-dev
-ENV CC gcc-8
-ENV CXX g++-8
-
-# Install CMake
-WORKDIR /tmp
-RUN wget https://cmake.org/files/v3.11/cmake-3.11.4.tar.gz
-RUN tar -xzvf cmake-3.11.4.tar.gz
-WORKDIR /tmp/cmake-3.11.4
-RUN ./bootstrap --prefix=/usr/local
-RUN make -j2
-RUN make install
-
-# Install Boost
-WORKDIR /tmp
-RUN wget -O boost_1_68_0.tar.gz http://sourceforge.net/projects/boost/files/boost/1.68.0/boost_1_68_0.tar.gz/download
-RUN tar xzvf boost_1_68_0.tar.gz
-WORKDIR /tmp/boost_1_68_0
-RUN ./bootstrap.sh --prefix=/usr/local --without-libraries=python,mpi
-RUN ./b2 -j2 toolset=gcc-8 cxxflags="-std=c++14"
-RUN ./b2 install
+    python3-pip
 
-# Install htslib
-WORKDIR /tmp
-RUN git clone -b master https://github.com/samtools/htslib.git
-WORKDIR /tmp/htslib
-RUN autoheader
-RUN autoconf
-RUN ./configure
-RUN make -j2
-RUN make install
+RUN pip3 install distro
 
 # Install Octopus
-WORKDIR /tmp
-RUN git clone -b develop https://github.com/luntergroup/octopus.git
-WORKDIR /tmp/octopus
-RUN ./scripts/install.py --root --threads=2
-RUN ldconfig
+COPY . /home/octopus
+RUN /home/octopus/scripts/install.py --dependencies --forests --threads 4
 
-WORKDIR /home
+ENTRYPOINT ["/home/octopus/bin/octopus"]