Merge branch 'release/0.7.1'

Author: Daniel Cooke

CMakeLists.txt

@@ -8,7 +8,7 @@ project(octopus)
 
 set(octopus_VERSION_MAJOR 0)
 set(octopus_VERSION_MINOR 7)
-set(octopus_VERSION_PATCH 0)
+set(octopus_VERSION_PATCH 1)
 set(octopus_VERSION_RELEASE "")
 
 # Generate list of compile commands.  This helps debugging and doesn't have a downside.
@@ -43,6 +43,7 @@ configure_file (
 include_directories(${CMAKE_BINARY_DIR}/generated)
 
 option(BUILD_SHARED_LIBS "Build the shared library" ON)
+set(COMPILER_ARCHITECTURE "native" CACHE STRING "Compiler -march argument")
 
 set(CMAKE_COLOR_MAKEFILE ON)
 

Dockerfile

@@ -1,6 +1,7 @@
 FROM ubuntu:latest
 
-ENV DEBIAN_FRONTEND=noninteractive
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Europe/London
 
 # Get all apt dependencies
 RUN apt-get -y update
@@ -17,7 +18,15 @@ RUN apt-get -y install \
 RUN pip3 install distro
 
 # Install Octopus
-COPY . /home/octopus
-RUN /home/octopus/scripts/install.py --dependencies --forests --threads 4
+ARG threads=4
+ARG architecture=haswell
+COPY . /opt/octopus
+RUN /opt/octopus/scripts/install.py \
+    --dependencies \
+    --forests \
+    --threads $threads \
+    --architecture $architecture
 
-ENTRYPOINT ["/home/octopus/bin/octopus"]
+ENV PATH="/opt/octopus/bin:${PATH}"
+
+ENTRYPOINT ["octopus"]

README.md

@@ -33,7 +33,7 @@ $ source ~/.bash_profile
 Call some variants:
 
 ```shell
-$ FOREST="$(pwd)/octopus/resources/forests/0.7.0/germline.v0.7.0.forest"
+$ FOREST="$(pwd)/octopus/resources/forests/germline.v0.7.0.forest"
 $ octopus -R hs37d5.fa -I NA12878.bam -T 1 to MT -o NA12878.octopus.vcf.gz --forest $FOREST --threads 8
 ```
 
@@ -43,7 +43,7 @@ Consult the [command line reference](https://github.com/luntergroup/octopus/wiki
 * A C++14 compiler with SSE2 support
 * A C++14 standard library implementation
 * Git 2.5 or greater
-* Boost 1.65 or greater
+* Boost 1.74 or greater
 * htslib 1.4 or greater
 * GMP 5.1.0 or greater
 * CMake 3.9 or greater

lib/CMakeLists.txt

@@ -1,2 +1,3 @@
 add_subdirectory(tandem)
-add_subdirectory(ranger)
+add_subdirectory(ranger)
+add_subdirectory(date)

lib/date/CMakeLists.txt

@@ -0,0 +1,20 @@
+set(DATE_SOURCES
+    date.h
+    tz.h
+    tz.cpp
+    tz_private.h
+    ios.h)
+
+add_library(date-tz STATIC ${DATE_SOURCES})
+
+set(WarningIgnores
+    -Wno-unused-parameter
+    -Wno-unused-function
+    -Wno-missing-braces)
+
+add_compile_options(-Wall -Wextra -Werror ${WarningIgnores})
+
+# find_package(CURL REQUIRED)
+# target_include_directories(date-tz SYSTEM PRIVATE ${CURL_INCLUDE_DIRS})
+# target_link_libraries(date-tz PRIVATE ${CURL_LIBRARIES})
+