Added tarball release as package option. Fixes #8, Fixes #18

statisticalbiotechnology · Dec 11, 2019 · 236b401 · 236b401
1 parent 48fb92a
commit 236b401
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Showing 9 changed files with 218 additions and 101 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -15,6 +15,11 @@ include("CommonCMake.txt")
 my_set(CMAKE_BUILD_TYPE "Debug" "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel.")
 #my_set(CMAKE_PREFIX_PATH "../" "Default path to packages")
 
+option(TARBALL_BUILD "Create a tarball instead of an installer package." OFF)
+if(TARBALL_BUILD)
+  add_definitions(-DTARBALL_BUILD) # triggers ifdef statements in the C++ code
+endif(TARBALL_BUILD)
+
 option(FINGERPRINT_FILTER "Use pre-filtering of spectrum pairs by their fragment fingerprints." OFF)
 if(FINGERPRINT_FILTER)
   add_definitions(-DFINGERPRINT_FILTER) # triggers ifdef statements in the C++ code

diff --git a/CPack.txt b/CPack.txt
@@ -62,53 +62,55 @@ if(UNIX)
   if(CMAKE_SYSTEM_NAME MATCHES "Linux")
     set(SPECIFIC_SYSTEM_VERSION_NAME "${CMAKE_SYSTEM_NAME}")
     set(CPACK_GENERATOR "TGZ")
-    if(EXISTS "/etc/redhat-release")
-      set(LINUX_NAME "")
-      file(READ "/etc/redhat-release" LINUX_ISSUE)
-    elseif(EXISTS "/etc/issue")
-      set(LINUX_NAME "")
-      file(READ "/etc/issue" LINUX_ISSUE)
-    endif()
-    if(DEFINED LINUX_ISSUE)
-      # Fedora case
-      if(LINUX_ISSUE MATCHES "Fedora")
-        string(REGEX MATCH "release ([0-9]+)" FEDORA "${LINUX_ISSUE}")
-        set(LINUX_NAME "FC${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "Fedora")
-      # Red Hat case
-      if(LINUX_ISSUE MATCHES "Red")
-        string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" REDHAT "${LINUX_ISSUE}")      
-        set(LINUX_NAME "RHEL_${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "Red")
-      # CentOS case
-      if(LINUX_ISSUE MATCHES "CentOS")
-        string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" CENTOS "${LINUX_ISSUE}")      
-        set(LINUX_NAME "CentOS_${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "CentOS")
-      # Ubuntu case
-      if(LINUX_ISSUE MATCHES "Ubuntu")
-        string(REGEX MATCH "buntu ([0-9]+\\.[0-9]+)" UBUNTU "${LINUX_ISSUE}")
-        set(LINUX_NAME "Ubuntu_${CMAKE_MATCH_1}")        
-        set(CPACK_GENERATOR "DEB")
-      endif(LINUX_ISSUE MATCHES "Ubuntu")
-      # Debian case
-      if(LINUX_ISSUE MATCHES "Debian")
-        string(REGEX MATCH "Debian .*ux ([a-zA-Z]*/?[a-zA-Z]*) .*" DEBIAN "${LINUX_ISSUE}")
-        set(LINUX_NAME "Debian_${CMAKE_MATCH_1}")
-        string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME}) 
-        set(CPACK_GENERATOR "DEB")       
-      endif(LINUX_ISSUE MATCHES "Debian")      
-      # Open SuSE case
-      if(LINUX_ISSUE MATCHES "SUSE")
-        string(REGEX MATCH "SUSE  ([0-9]+\\.[0-9]+)" SUSE "${LINUX_ISSUE}")
-        set(LINUX_NAME "openSUSE_${CMAKE_MATCH_1}")
-        string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME})   
-        set(CPACK_GENERATOR "RPM")     
-      endif(LINUX_ISSUE MATCHES "SUSE")
-    endif(DEFINED LINUX_ISSUE)      
+    if(NOT TARBALL_BUILD)
+      if(EXISTS "/etc/redhat-release")
+        set(LINUX_NAME "")
+        file(READ "/etc/redhat-release" LINUX_ISSUE)
+      elseif(EXISTS "/etc/issue")
+        set(LINUX_NAME "")
+        file(READ "/etc/issue" LINUX_ISSUE)
+      endif()
+      if(DEFINED LINUX_ISSUE)
+        # Fedora case
+        if(LINUX_ISSUE MATCHES "Fedora")
+          string(REGEX MATCH "release ([0-9]+)" FEDORA "${LINUX_ISSUE}")
+          set(LINUX_NAME "FC${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "Fedora")
+        # Red Hat case
+        if(LINUX_ISSUE MATCHES "Red")
+          string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" REDHAT "${LINUX_ISSUE}")      
+          set(LINUX_NAME "RHEL_${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "Red")
+        # CentOS case
+        if(LINUX_ISSUE MATCHES "CentOS")
+          string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" CENTOS "${LINUX_ISSUE}")      
+          set(LINUX_NAME "CentOS_${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "CentOS")
+        # Ubuntu case
+        if(LINUX_ISSUE MATCHES "Ubuntu")
+          string(REGEX MATCH "buntu ([0-9]+\\.[0-9]+)" UBUNTU "${LINUX_ISSUE}")
+          set(LINUX_NAME "Ubuntu_${CMAKE_MATCH_1}")        
+          set(CPACK_GENERATOR "DEB")
+        endif(LINUX_ISSUE MATCHES "Ubuntu")
+        # Debian case
+        if(LINUX_ISSUE MATCHES "Debian")
+          string(REGEX MATCH "Debian .*ux ([a-zA-Z]*/?[a-zA-Z]*) .*" DEBIAN "${LINUX_ISSUE}")
+          set(LINUX_NAME "Debian_${CMAKE_MATCH_1}")
+          string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME}) 
+          set(CPACK_GENERATOR "DEB")       
+        endif(LINUX_ISSUE MATCHES "Debian")      
+        # Open SuSE case
+        if(LINUX_ISSUE MATCHES "SUSE")
+          string(REGEX MATCH "SUSE  ([0-9]+\\.[0-9]+)" SUSE "${LINUX_ISSUE}")
+          set(LINUX_NAME "openSUSE_${CMAKE_MATCH_1}")
+          string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME})   
+          set(CPACK_GENERATOR "RPM")     
+        endif(LINUX_ISSUE MATCHES "SUSE")
+      endif(DEFINED LINUX_ISSUE)     
+    endif(NOT TARBALL_BUILD) 
   endif(CMAKE_SYSTEM_NAME MATCHES "Linux")
 endif(UNIX)
 

diff --git a/admin/builders/install_qt.sh b/admin/builders/install_qt.sh
@@ -3,11 +3,11 @@ tools_dir=$1
 # change directory to the build director
 cd ${tools_dir}
 
-linux_qt=qtbase-everywhere-src-5.11.2
+linux_qt=qtbase-everywhere-src-5.13.2
 if [ ! -d Qt-dynamic ]; then
 
   if [ ! -f ${linux_qt}.tar.xz ]; then
-    wget http://download.qt.io/official_releases/qt/5.11/5.11.2/submodules/${linux_qt}.tar.xz
+    wget http://download.qt.io/official_releases/qt/5.13/5.13.2/submodules/${linux_qt}.tar.xz
   fi
 
   tar xf ${linux_qt}.tar.xz

diff --git a/admin/builders/tarball64_build.sh b/admin/builders/tarball64_build.sh
@@ -0,0 +1,96 @@
+#!/bin/bash
+# managing input arguments
+while getopts “s:b:r:t:g” OPTION; do
+  case $OPTION in
+    s) src_dir=${OPTARG};;
+    t) branch=${OPTARG};;
+    r) release_dir=${OPTARG};;
+    b) build_dir=${OPTARG};;
+    g) no_gui=true;;
+    \?) echo "Invalid option: -${OPTARG}" >&2;;
+  esac
+done
+
+if [[ -z ${build_dir} ]]; then
+  build_dir="$(mktemp -d --tmpdir build_XXXX)";
+fi
+if [[ -z ${src_dir} ]]; then
+  if [[ -n  ${branch} ]]; then
+    sudo apt-get install git;
+    src_dir="$(mktemp -d --tmpdir build_XXXX)";
+    git clone --branch "$1" https://github.com/statisticalbiotechnology/maracluster.git "${src_dir}/maracluster";
+  else
+    src_dir=$(dirname ${BASH_SOURCE})/../../../
+  fi
+fi
+if [[ -z ${release_dir} ]]; then
+  release_dir=${HOME}/release
+fi
+
+rm -f $build_dir/{maracluster,maracluster-gui}/mar*.tar.gz
+
+sudo apt-get update;
+sudo apt-get upgrade;
+sudo apt-get -y install g++ make cmake
+CMAKE_BINARY=cmake # this can be overridden if a newer version of cmake is needed
+
+mkdir -p ${build_dir}/tools
+cd ${build_dir}/tools
+
+if [ ! -d ${build_dir}/tools/proteowizard ]; then
+  ${src_dir}/maracluster/admin/builders/install_proteowizard.sh ${build_dir}/tools
+fi
+
+#-----MaRaCluster-GUI dependencies-------
+
+if [ "$no_gui" != true ] ; then
+  # patchelf is available from Ubuntu 16.04, install from source otherwise
+  sudo apt -y install patchelf || missing_patchelf=true
+  if [ "$missing_patchelf" == true ] ; then
+    if [ ! -d ${build_dir}/tools/patchelf-0.8 ]; then
+      wget http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.bz2
+      tar xf patchelf-0.8.tar.bz2
+      cd patchelf-0.8/
+      ./configure --prefix="${build_dir}/tools"
+      make install
+    fi
+    patchelf_binary=${build_dir}/tools/bin/patchelf
+  else
+    patchelf_binary=patchelf
+  fi
+
+  sudo apt -y install libgl1-mesa-dev libicu-dev libfreetype6-dev
+
+  source ${src_dir}/maracluster/admin/builders/install_qt.sh ${build_dir}/tools
+fi
+
+mkdir -p $build_dir/maracluster
+#-----cmake-----
+cd $build_dir/maracluster;
+echo -n "cmake maracluster.....";
+${CMAKE_BINARY} -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DTARBALL_BUILD=ON -DCMAKE_INSTALL_PREFIX="" -DCMAKE_PREFIX_PATH=$build_dir/tools $src_dir/maracluster;
+#-----make------
+echo -n "make maracluster (this will take few minutes).....";
+make -j 4;
+make -j 4 package;
+
+mkdir -p $release_dir
+cp -v $build_dir/maracluster/mar*.tar.gz $release_dir
+
+if [ "$no_gui" != true ] ; then
+  #######maracluster-gui########
+  mkdir -p $build_dir/maracluster-gui
+  cd $build_dir/maracluster-gui
+  #-----cmake-----
+  echo -n "cmake maracluster-gui.....";
+  ${CMAKE_BINARY} -DTARGET_ARCH=amd64 -DCMAKE_BUILD_TYPE=Release -DTARBALL_BUILD=ON -DCMAKE_INSTALL_PREFIX="" -DCMAKE_PREFIX_PATH="$build_dir/tools/;$build_dir/tools/Qt-dynamic/" $src_dir/maracluster/src/qt-gui;
+
+  #-----make------
+  echo -n "make maracluster-gui (this will take few minutes).....";
+
+  make -j 4;
+  make -j 4 package;
+
+  cp -v $build_dir/maracluster-gui/mar*.tar.gz $release_dir
+fi
+
diff --git a/admin/vagrant/batch.sh b/admin/vagrant/batch.sh
@@ -10,8 +10,9 @@ platforms=()
 #platforms+=(win64)
 #platforms+=(win32)
 #platforms+=(centos)
-platforms+=(fedora)
-platforms+=(ubuntu)
+#platforms+=(fedora)
+#platforms+=(ubuntu)
+platforms+=(tarball)
 
 for platform in ${platforms[@]}; do
   echo "Building $platform binaries"

diff --git a/admin/vagrant/manager.sh b/admin/vagrant/manager.sh
@@ -44,6 +44,12 @@ while getopts “hab:s:r:p:” OPTION; do
         s)  src=$OPTARG;;
         r)  release=$OPTARG;;
         p)  case $OPTARG in
+               	tarball)
+               	    post="tarball64"
+                    vagbox_name="ubuntu/trusty64"
+                    vagbox_url=""
+                    package_ext="tar.gz"
+                    ;;
                	ubuntu)
                     post="ubuntu64"
                     vagbox_name="ubuntu/trusty64"

diff --git a/quickbuild.sh b/quickbuild.sh
@@ -25,14 +25,17 @@ EOF
 }
 
 skip_gui=""
-while getopts “hs:b:r:p:” OPTION; do
+while getopts “hs:b:r:p:g” OPTION; do
     case $OPTION in
         h)  usage;exit 1;;
         s)  src_dir=$OPTARG;;
         b)  build_dir=$OPTARG;;
         r)  release_dir=$OPTARG;;
         g)  skip_gui="-g";;
         p)  case $OPTARG in
+               	tarball)
+               	    post="tarball64"
+               	    ;;
                	ubuntu)
                     post="ubuntu64"
                     ;;

diff --git a/src/qt-gui/CMakeLists.txt b/src/qt-gui/CMakeLists.txt
@@ -108,6 +108,8 @@ elseif (UNIX)
   find_package(ICU REQUIRED COMPONENTS uc i18n data)
   find_package(Freetype REQUIRED)
   find_library(STDCPP_LIBRARY NAMES libstdc++.so.6 )
+  find_library(PCRE2_16_LIBRARY NAMES libpcre2-16.so )
+  find_library(PNG_12_LIBRARY NAMES libpng12.so.0 )
 
   set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES_BACKUP})  
 
@@ -124,7 +126,7 @@ elseif (UNIX)
   _qt5_get_shared_library(Gui)
   _qt5_get_shared_library(DBus)
 
-  foreach (LIBRARY ${ICU_LIBRARIES} ${FREETYPE_LIBRARIES} ${QtXcbQpa_LIBRARY_FULL} ${STDCPP_LIBRARY})
+  foreach (LIBRARY ${ICU_LIBRARIES} ${FREETYPE_LIBRARIES} ${QtXcbQpa_LIBRARY_FULL} ${STDCPP_LIBRARY} ${PCRE2_16_LIBRARY} ${PNG_12_LIBRARY})
     get_filename_component(LIBRARY_RESOLVED ${LIBRARY} REALPATH)
     list(APPEND LIBRARIES_RESOLVED ${LIBRARY_RESOLVED})
     string(REGEX REPLACE "(.*\\.so.[0-9]+).*" "\\1" LIBRARY_MAIN_VERSION "${LIBRARY_RESOLVED}")
@@ -144,7 +146,7 @@ elseif (UNIX)
   find_program (PATCHELF_BINARY NAMES patchelf)
   message( STATUS "Found patchelf binary: ${PATCHELF_BINARY}")
   install(CODE "execute_process(COMMAND ${PATCHELF_BINARY} --remove-rpath ${QtXcbPlugin_copied_location})") # gives "stat: No such file or directory" error on earlier versions of patchelf. This can be ignored.
-  install(CODE "execute_process(COMMAND ${PATCHELF_BINARY} --force-rpath --set-rpath '$ORIGIN/..' ${QtXcbPlugin_copied_location})")
+  install(CODE "execute_process(COMMAND ${PATCHELF_BINARY} --force-rpath --set-rpath $ORIGIN/.. ${QtXcbPlugin_copied_location})")
 
   install(PROGRAMS ${QtXcbPlugin_copied_location} DESTINATION lib/maracluster/platforms)
 

diff --git a/src/qt-gui/CPack.txt b/src/qt-gui/CPack.txt
@@ -44,53 +44,55 @@ if(UNIX)
   if(CMAKE_SYSTEM_NAME MATCHES "Linux")
     set(SPECIFIC_SYSTEM_VERSION_NAME "${CMAKE_SYSTEM_NAME}")
     set(CPACK_GENERATOR "TGZ")
-    if(EXISTS "/etc/redhat-release")
-      set(LINUX_NAME "")
-      file(READ "/etc/redhat-release" LINUX_ISSUE)
-    elseif(EXISTS "/etc/issue")
-      set(LINUX_NAME "")
-      file(READ "/etc/issue" LINUX_ISSUE)
-    endif()
-    if(DEFINED LINUX_ISSUE)
-      # Fedora case
-      if(LINUX_ISSUE MATCHES "Fedora")
-        string(REGEX MATCH "release ([0-9]+)" FEDORA "${LINUX_ISSUE}")
-        set(LINUX_NAME "FC${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "Fedora")
-      # Red Hat case
-      if(LINUX_ISSUE MATCHES "Red")
-        string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" REDHAT "${LINUX_ISSUE}")      
-        set(LINUX_NAME "RHEL_${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "Red")
-      # CentOS case
-      if(LINUX_ISSUE MATCHES "CentOS")
-        string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" CENTOS "${LINUX_ISSUE}")      
-        set(LINUX_NAME "CentOS_${CMAKE_MATCH_1}")  
-        set(CPACK_GENERATOR "RPM")      
-      endif(LINUX_ISSUE MATCHES "CentOS")
-      # Ubuntu case
-      if(LINUX_ISSUE MATCHES "Ubuntu")
-        string(REGEX MATCH "buntu ([0-9]+\\.[0-9]+)" UBUNTU "${LINUX_ISSUE}")
-        set(LINUX_NAME "Ubuntu_${CMAKE_MATCH_1}")        
-        set(CPACK_GENERATOR "DEB")
-      endif(LINUX_ISSUE MATCHES "Ubuntu")
-      # Debian case
-      if(LINUX_ISSUE MATCHES "Debian")
-        string(REGEX MATCH "Debian .*ux ([a-zA-Z]*/?[a-zA-Z]*) .*" DEBIAN "${LINUX_ISSUE}")
-        set(LINUX_NAME "Debian_${CMAKE_MATCH_1}")
-        string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME}) 
-        set(CPACK_GENERATOR "DEB")       
-      endif(LINUX_ISSUE MATCHES "Debian")      
-      # Open SuSE case
-      if(LINUX_ISSUE MATCHES "SUSE")
-        string(REGEX MATCH "SUSE  ([0-9]+\\.[0-9]+)" SUSE "${LINUX_ISSUE}")
-        set(LINUX_NAME "openSUSE_${CMAKE_MATCH_1}")
-        string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME})   
-        set(CPACK_GENERATOR "RPM")     
-      endif(LINUX_ISSUE MATCHES "SUSE")
-    endif(DEFINED LINUX_ISSUE)      
+    if(NOT TARBALL_BUILD)
+      if(EXISTS "/etc/redhat-release")
+        set(LINUX_NAME "")
+        file(READ "/etc/redhat-release" LINUX_ISSUE)
+      elseif(EXISTS "/etc/issue")
+        set(LINUX_NAME "")
+        file(READ "/etc/issue" LINUX_ISSUE)
+      endif()
+      if(DEFINED LINUX_ISSUE)
+        # Fedora case
+        if(LINUX_ISSUE MATCHES "Fedora")
+          string(REGEX MATCH "release ([0-9]+)" FEDORA "${LINUX_ISSUE}")
+          set(LINUX_NAME "FC${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "Fedora")
+        # Red Hat case
+        if(LINUX_ISSUE MATCHES "Red")
+          string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" REDHAT "${LINUX_ISSUE}")      
+          set(LINUX_NAME "RHEL_${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "Red")
+        # CentOS case
+        if(LINUX_ISSUE MATCHES "CentOS")
+          string(REGEX MATCH "release ([0-9]+\\.[0-9]+)" CENTOS "${LINUX_ISSUE}")      
+          set(LINUX_NAME "CentOS_${CMAKE_MATCH_1}")  
+          set(CPACK_GENERATOR "RPM")      
+        endif(LINUX_ISSUE MATCHES "CentOS")
+        # Ubuntu case
+        if(LINUX_ISSUE MATCHES "Ubuntu")
+          string(REGEX MATCH "buntu ([0-9]+\\.[0-9]+)" UBUNTU "${LINUX_ISSUE}")
+          set(LINUX_NAME "Ubuntu_${CMAKE_MATCH_1}")        
+          set(CPACK_GENERATOR "DEB")
+        endif(LINUX_ISSUE MATCHES "Ubuntu")
+        # Debian case
+        if(LINUX_ISSUE MATCHES "Debian")
+          string(REGEX MATCH "Debian .*ux ([a-zA-Z]*/?[a-zA-Z]*) .*" DEBIAN "${LINUX_ISSUE}")
+          set(LINUX_NAME "Debian_${CMAKE_MATCH_1}")
+          string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME}) 
+          set(CPACK_GENERATOR "DEB")       
+        endif(LINUX_ISSUE MATCHES "Debian")      
+        # Open SuSE case
+        if(LINUX_ISSUE MATCHES "SUSE")
+          string(REGEX MATCH "SUSE  ([0-9]+\\.[0-9]+)" SUSE "${LINUX_ISSUE}")
+          set(LINUX_NAME "openSUSE_${CMAKE_MATCH_1}")
+          string(REPLACE "/" "_" LINUX_NAME ${LINUX_NAME})   
+          set(CPACK_GENERATOR "RPM")     
+        endif(LINUX_ISSUE MATCHES "SUSE")
+      endif(DEFINED LINUX_ISSUE)
+    endif(NOT TARBALL_BUILD)
   endif(CMAKE_SYSTEM_NAME MATCHES "Linux")
 endif(UNIX)