Fixed vagrant builds for all platforms, ready for v0.2 release. Fixes #1

statisticalbiotechnology · May 27, 2019 · 59e0c95 · 59e0c95
1 parent edb9d0b
commit 59e0c95
Show file tree

Hide file tree

Showing 14 changed files with 91 additions and 205 deletions.
diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,5 @@
 *.exe
 *.out
 *.app
+
+admin/vagrant/*_output.txt
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -88,6 +88,8 @@ else (MSVC)
   set(MVN_CMD mvn)
 endif (MSVC)
 
+MESSAGE( STATUS "Building Dinosaur with Maven" )
+
 execute_process(COMMAND ${MVN_CMD} package -Pconf -DskipTests -Ddir=${CMAKE_CURRENT_BINARY_DIR}/dinosaur WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/ext/dinosaur OUTPUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/dinosaur_maven_stdout.txt ERROR_FILE ${CMAKE_CURRENT_BINARY_DIR}/dinosaur_maven_stderr.txt RESULT_VARIABLE MVN_RESULT)
 
 if(NOT "${MVN_RESULT}" STREQUAL "0")

diff --git a/CommonCMake.txt b/CommonCMake.txt
@@ -59,7 +59,7 @@ set(CMAKE_MODULE_PATH ${QUANDENSER_SOURCE_DIR}/cmake)
 
 # VERSION AND NAMESPACES
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "01")
+set(CPACK_PACKAGE_VERSION_MINOR "02")
 set(CPACK_PACKAGE_VERSION_PATCH "0")
 
 # UPDATE PATCH VERSION FOR INTERMEDIATE BUILDS
@@ -128,7 +128,9 @@ set(Boost_USE_STATIC_RUNTIME ON)
 set(BOOST_MIN_VERSION "1.43.0")
 set(Boost_ADDITIONAL_VERSIONS "1.43.0")
 
-add_definitions(-DBOOST_NO_CXX11_VARIADIC_TEMPLATES)
+if(NOT APPLE)
+  add_definitions(-DBOOST_NO_CXX11_VARIADIC_TEMPLATES)
+endif(NOT APPLE)
 
 ###############################################################################
 # SET SHARED DYNAMIC LINKING LIBRARIES

diff --git a/admin/builders/centos64_build.sh b/admin/builders/centos64_build.sh
@@ -26,60 +26,14 @@ if [[ -z ${release_dir} ]]; then
   release_dir=${HOME}/release
 fi
 
-sudo yum install -y gcc gcc-c++ rpm-build cmake
+sudo yum install -y gcc gcc-c++ rpm-build cmake rsync
+sudo yum install -y java-1.8.0-openjdk-devel maven
 
 mkdir -p ${build_dir}/tools
 cd ${build_dir}/tools
 
 if [ ! -d ${build_dir}/tools/proteowizard ]; then
-  echo "Download source code for ProteoWizard from their SVN repository"
-  sudo yum install -y subversion
-  rev=9393
-  svn co -r ${rev} --depth immediates https://svn.code.sf.net/p/proteowizard/code/trunk/pwiz ./proteowizard
-  svn update -r ${rev} --set-depth infinity ./proteowizard/pwiz
-  svn update -r ${rev} --set-depth infinity ./proteowizard/libraries
-
-  # install and keep libraries in the libs folder of this project for linking
-  cd proteowizard
-
-  ./clean.sh
-
-  echo "Building ProteoWizard and Boost, this may take some time.."
-
-  ./quickbuild.sh --without-binary-msdata \
-                  pwiz/data/common//pwiz_data_common \
-                  pwiz/data/identdata//pwiz_data_identdata \
-                  pwiz/data/identdata//pwiz_data_identdata_version \
-                  pwiz/data/msdata//pwiz_data_msdata \
-                  pwiz/data/msdata//pwiz_data_msdata_version \
-                  pwiz/data/proteome//pwiz_data_proteome \
-                  pwiz/utility/chemistry//pwiz_utility_chemistry \
-                  pwiz/utility/minimxml//pwiz_utility_minimxml \
-                  pwiz/utility/misc//SHA1 \
-                  pwiz/utility/misc//pwiz_utility_misc \
-                  /ext/zlib//z \
-                  /ext/boost//system \
-                  /ext/boost//thread \
-                  /ext/boost//chrono \
-                  /ext/boost//regex \
-                  /ext/boost//filesystem \
-                  /ext/boost//iostreams \
-                  /ext/boost//program_options \
-                  /ext/boost//serialization \
-                  > ../pwiz_installation.log 2>&1
-
-  # for revision 7692 the "libraries" target does not work, so we have to copy everything manually
-  mkdir -p ../lib
-  find build-linux-x86_64/ -type f | grep -i .a$ | xargs -i cp {} ../lib
-
-  mkdir -p ../include
-  find pwiz/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../include/
-
-  cd libraries/boost_1_56_0/
-  find boost/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
-
-  cd ../zlib-1.2.3
-  find ./ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
+  ${src_dir}/quandenser/ext/maracluster/admin/builders/install_proteowizard.sh ${build_dir}/tools
 fi
 
 mkdir -p $build_dir/quandenser

diff --git a/admin/builders/fedora64_build.sh b/admin/builders/fedora64_build.sh
@@ -27,59 +27,13 @@ if [[ -z ${release_dir} ]]; then
 fi
 
 sudo dnf install -y gcc gcc-c++ rpm-build cmake
+sudo dnf install -y java-1.8.0-openjdk.x86_64 maven
 
 mkdir -p ${build_dir}/tools
 cd ${build_dir}/tools
 
 if [ ! -d ${build_dir}/tools/proteowizard ]; then
-  echo "Download source code for ProteoWizard from their SVN repository"
-  sudo dnf install -y subversion
-  rev=9393
-  svn co -r ${rev} --depth immediates https://svn.code.sf.net/p/proteowizard/code/trunk/pwiz ./proteowizard
-  svn update -r ${rev} --set-depth infinity ./proteowizard/pwiz
-  svn update -r ${rev} --set-depth infinity ./proteowizard/libraries
-
-  # install and keep libraries in the libs folder of this project for linking
-  cd proteowizard
-
-  ./clean.sh
-
-  echo "Building ProteoWizard and Boost, this may take some time.."
-
-  ./quickbuild.sh --without-binary-msdata \
-                  pwiz/data/common//pwiz_data_common \
-                  pwiz/data/identdata//pwiz_data_identdata \
-                  pwiz/data/identdata//pwiz_data_identdata_version \
-                  pwiz/data/msdata//pwiz_data_msdata \
-                  pwiz/data/msdata//pwiz_data_msdata_version \
-                  pwiz/data/proteome//pwiz_data_proteome \
-                  pwiz/utility/chemistry//pwiz_utility_chemistry \
-                  pwiz/utility/minimxml//pwiz_utility_minimxml \
-                  pwiz/utility/misc//SHA1 \
-                  pwiz/utility/misc//pwiz_utility_misc \
-                  /ext/zlib//z \
-                  /ext/boost//system \
-                  /ext/boost//thread \
-                  /ext/boost//chrono \
-                  /ext/boost//regex \
-                  /ext/boost//filesystem \
-                  /ext/boost//iostreams \
-                  /ext/boost//program_options \
-                  /ext/boost//serialization \
-                  > ../pwiz_installation.log 2>&1
-
-  # for revision 7692 the "libraries" target does not work, so we have to copy everything manually
-  mkdir -p ../lib
-  find build-linux-x86_64/ -type f | grep -i .a$ | xargs -i cp {} ../lib
-
-  mkdir -p ../include
-  find pwiz/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../include/
-
-  cd libraries/boost_1_56_0/
-  find boost/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
-
-  cd ../zlib-1.2.3
-  find ./ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
+  ${src_dir}/quandenser/ext/maracluster/admin/builders/install_proteowizard.sh ${build_dir}/tools
 fi
 
 mkdir -p $build_dir/quandenser

diff --git a/admin/builders/nativew32_build.bat b/admin/builders/nativew32_build.bat
@@ -152,7 +152,7 @@ if not exist "%PWIZ_DIR%\lib" (
 set MVN_BASE=apache-maven-3.6.1
 set MVN_URL=http://ftp.unicamp.br/pub/apache/maven/maven-3/3.6.1/binaries/%MVN_BASE%-bin.zip
 if not exist "%INSTALL_DIR%\%MVN_BASE%" (
-  echo Downloading and installing CMake
+  echo Downloading and installing Maven
   call :downloadfile %MVN_URL% %INSTALL_DIR%\mvn.zip
   %ZIP_EXE% x "%INSTALL_DIR%\mvn.zip" -o"%INSTALL_DIR%" > NUL
 )

diff --git a/admin/builders/nativew64_build.bat b/admin/builders/nativew64_build.bat
@@ -159,7 +159,7 @@ if not exist "%PWIZ_DIR%\lib" (
 set MVN_BASE=apache-maven-3.6.1
 set MVN_URL=http://ftp.unicamp.br/pub/apache/maven/maven-3/3.6.1/binaries/%MVN_BASE%-bin.zip
 if not exist "%INSTALL_DIR%\%MVN_BASE%" (
-  echo Downloading and installing CMake
+  echo Downloading and installing Maven
   call :downloadfile %MVN_URL% %INSTALL_DIR%\mvn.zip
   %ZIP_EXE% x "%INSTALL_DIR%\mvn.zip" -o"%INSTALL_DIR%" > NUL
 )

diff --git a/admin/builders/osx64_build.sh b/admin/builders/osx64_build.sh
@@ -44,12 +44,20 @@ if [[ -d /opt/local/var/macports ]]
   then
     echo "[ Package manager ] : MacPorts "
     package_manager="sudo port"
-    other_packages="cmake gnutar"
-elif [[ -f ${HOME}/bin/brew ]]
+    other_packages="cmake gnutar wget maven32 openjdk8"
+elif [[ -f ${HOME}/bin/brew ]] || [[ -f /usr/local/bin/brew ]]
   then
     echo "[ Package manager ] : Homebrew "
-    package_manager=$HOME/bin/brew
-    other_packages="cmake gnutar"
+    if [[ -f ${HOME}/bin/brew ]]
+      then
+        package_manager=$HOME/bin/brew
+    else
+      package_manager=brew
+    fi
+    other_packages="cmake gnu-tar wget maven"
+    ${package_manager} update || true # brew.rb raises an error on the vagrant box, just ignore it
+    ${package_manager} tap AdoptOpenJDK/openjdk
+    ${package_manager} cask install adoptopenjdk8
 else
     package_manager_installed=false
 fi
@@ -93,50 +101,7 @@ mkdir -p ${build_dir}/tools
 cd ${build_dir}/tools
 
 if [ ! -d ${build_dir}/tools/proteowizard ]; then
-  echo "Download source code for ProteoWizard from their SVN repository"
-  $package_manager install subversion
-  rev=9393
-  svn co -r ${rev} --depth immediates https://svn.code.sf.net/p/proteowizard/code/trunk/pwiz ./proteowizard
-  svn update -r ${rev} --set-depth infinity ./proteowizard/pwiz
-  svn update -r ${rev} --set-depth infinity ./proteowizard/libraries
-
-  # install and keep libraries in the libs folder of this project for linking
-  cd proteowizard
-
-  ./clean.sh
-
-  echo "Building ProteoWizard and Boost, this may take some time.."
-
-  # if you have more than 4GB of memory available, you could try to use more than 2 cores to speed things up
-  ./quickbuild.sh -j4 --without-binary-msdata \
-                  pwiz/data/common//pwiz_data_common \
-                  pwiz/data/identdata//pwiz_data_identdata \
-                  pwiz/data/identdata//pwiz_data_identdata_version \
-                  pwiz/data/msdata//pwiz_data_msdata \
-                  pwiz/data/msdata//pwiz_data_msdata_version \
-                  pwiz/data/proteome//pwiz_data_proteome \
-                  pwiz/utility/chemistry//pwiz_utility_chemistry \
-                  pwiz/utility/minimxml//pwiz_utility_minimxml \
-                  pwiz/utility/misc//SHA1 \
-                  pwiz/utility/misc//pwiz_utility_misc \
-                  /ext/zlib//z \
-                  /ext/boost//system \
-                  /ext/boost//thread \
-                  /ext/boost//chrono \
-                  /ext/boost//regex \
-                  /ext/boost//filesystem \
-                  /ext/boost//iostreams \
-                  /ext/boost//program_options \
-                  /ext/boost//serialization \
-                  > ../pwiz_installation.log 2>&1
-
-  # for revision 7692 the "libraries" target does not work, so we have to copy everything manually
-  mkdir -p ../lib
-  find build-macosx-x86_64/ -type f | grep -i .a$ | xargs -I{} cp {} ../lib
-
-  mkdir -p ../include
-  rsync -ap --include "*/" --include "*.h" --include "*.hpp" --include "*.ipp" --exclude "*" pwiz libraries/boost_1_56_0/boost libraries/boost_aux/boost ../include/
-  rsync -ap --include "*/" --include "*.h" --include "*.hpp" --exclude "*"  libraries/zlib-1.2.3/ ../include/zlib
+  ${src_dir}/quandenser/ext/maracluster/admin/builders/install_proteowizard.sh ${build_dir}/tools
 fi
 
 #-------------------------------------------

diff --git a/admin/builders/ubuntu64_build.sh b/admin/builders/ubuntu64_build.sh
@@ -28,61 +28,13 @@ fi
 
 sudo apt-get update;
 sudo apt-get upgrade;
-sudo apt-get -y install g++ make cmake maven
+sudo apt-get -y install g++ make cmake maven openjdk-8-jdk
 
 mkdir -p ${build_dir}/tools
 cd ${build_dir}/tools
 
 if [ ! -d ${build_dir}/tools/proteowizard ]; then
-  echo "Download source code for ProteoWizard from their SVN repository"
-  sudo apt-get -y install subversion
-  rev=9393
-  svn co -r ${rev} --depth immediates https://svn.code.sf.net/p/proteowizard/code/trunk/pwiz ./proteowizard
-  svn update -r ${rev} --set-depth infinity ./proteowizard/pwiz
-  svn update -r ${rev} --set-depth infinity ./proteowizard/libraries
-
-  # install and keep libraries in the libs folder of this project for linking
-  cd proteowizard
-
-  ./clean.sh
-
-  echo "Building ProteoWizard and Boost, this may take some time.."
-
-  # if you have more than 4GB of memory available, you could try to use more than 2 cores to speed things up
-  ./quickbuild.sh -j2 --without-binary-msdata \
-                  pwiz/data/common//pwiz_data_common \
-                  pwiz/data/identdata//pwiz_data_identdata \
-                  pwiz/data/identdata//pwiz_data_identdata_version \
-                  pwiz/data/msdata//pwiz_data_msdata \
-                  pwiz/data/msdata//pwiz_data_msdata_version \
-                  pwiz/data/proteome//pwiz_data_proteome \
-                  pwiz/utility/chemistry//pwiz_utility_chemistry \
-                  pwiz/utility/minimxml//pwiz_utility_minimxml \
-                  pwiz/utility/misc//SHA1 \
-                  pwiz/utility/misc//pwiz_utility_misc \
-                  /ext/zlib//z \
-                  /ext/boost//system \
-                  /ext/boost//thread \
-                  /ext/boost//chrono \
-                  /ext/boost//regex \
-                  /ext/boost//filesystem \
-                  /ext/boost//iostreams \
-                  /ext/boost//program_options \
-                  /ext/boost//serialization \
-                  > ../pwiz_installation.log 2>&1
-
-  # for revision 7692 the "libraries" target does not work, so we have to copy everything manually
-  mkdir -p ../lib
-  find build-linux-x86_64/ -type f | grep -i .a$ | xargs -i cp {} ../lib
-
-  mkdir -p ../include
-  find pwiz/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../include/
-
-  cd libraries/boost_1_56_0/
-  find boost/ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
-
-  cd ../zlib-1.2.3
-  find ./ -type f | grep -i '.h$\|.hpp$' | xargs -i cp --parents {} ../../../include/
+  ${src_dir}/quandenser/ext/maracluster/admin/builders/install_proteowizard.sh ${build_dir}/tools
 fi
 
 mkdir -p $build_dir/quandenser

diff --git a/admin/vagrant/manager.sh b/admin/vagrant/manager.sh
@@ -52,7 +52,7 @@ while getopts “hab:s:r:p:” OPTION; do
         p)  case $OPTARG in
                	ubuntu)
                     post="ubuntu64"
-                    vagbox_name="ubuntu/trusty64"
+                    vagbox_name="ubuntu/xenial64"
                     vagbox_url=""
                     package_ext="deb"
                     ;;
@@ -201,7 +201,7 @@ Vagrant.configure("2") do |config|
     :export_options => ['async,insecure,no_subtree_check,no_acl,no_root_squash']
 
   config.vm.provider "virtualbox" do |vb|
-    vb.customize ["modifyvm", :id, "--memory", "4096", "--cpus", "4"]
+    vb.customize ["modifyvm", :id, "--memory", "8192", "--cpus", "4"]
     # vb.gui = true # turn on for trouble shooting, e.g. if boot times out repeatedly
     # Fix "hfs mounted macintosh hd on device root_device" issue
     vb.customize ["modifyvm", :id, "--cpuidset", "1","000206a7","02100800","1fbae3bf","bfebfbff"]
@@ -240,7 +240,7 @@ Vagrant.configure("2") do |config|
   config.ssh.insert_key = false
   config.vm.boot_timeout = 600
   config.vm.provider "virtualbox" do |vb|
-    vb.customize ["modifyvm", :id, "--memory", "4096", "--cpus", "4"]
+    vb.customize ["modifyvm", :id, "--memory", "8192", "--cpus", "4"]
     # vb.gui = true # turn on for trouble shooting, e.g. if boot times out repeatedly
   end
   config.vm.provision :shell do |shell|

diff --git a/ext/maracluster b/ext/maracluster
diff --git a/src/DinosaurIO.cpp b/src/DinosaurIO.cpp
@@ -19,8 +19,8 @@
 
 namespace quandenser {
 
-const std::string DinosaurIO::kAdvancedParamFile = std::string(JAR_PATH) + std::string("advParams_dinosaur_targeted.txt");
-const std::string DinosaurIO::kDinosaurJar = std::string(JAR_PATH) + std::string("Dinosaur-1.1.3.free.jar");
+const std::string DinosaurIO::kAdvancedParamFile = "\"" + Globals::getJarPath() + std::string("advParams_dinosaur_targeted.txt") + "\"";
+const std::string DinosaurIO::kDinosaurJar = "\"" + Globals::getJarPath() + std::string("Dinosaur-1.1.3.free.jar") + "\"";
 
 std::string DinosaurIO::javaMemory_ = "24000M";
 int DinosaurIO::javaNumThreads_ = 4;
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,3 +30,5 @@ @@
     *.exe
     *.out
     *.app
+    admin/vagrant/*_output.txt