Fixed some more build errors and updated ReadMe

ReadMe.md

@@ -4,14 +4,22 @@ This repository holds the source code for clustering and merging of fragment spe
 
 ### Installation
 
-Installers for several operating systems can be found on the [Release page](https://github.com/statisticalbiotechnology/maracluster/releases).
+Installers for several operating systems can be found on the [Release page](https://github.com/statisticalbiotechnology/maracluster/releases). Both a command line as well as a graphical user interface are available for all platforms.
 
 If you prefer to compile from source, or are running on a different operating system, [click here](#installation-from-source).
 
-### Interface
+### Example
 
 An example, including spectrum files and a shell script, can be downloaded from http://kaell.org/files/maracluster_sample.zip.
 
+### Graphical User Interface (GUI)
+
+To run the example, simply select the spectrum files after clicking the `Add ms2 files` button, select an output folder and click the `Run MaRaCluster` button.
+
+A more elaborate guide for using the GUI can be found from the Help menu in the menu bar of the GUI.
+
+### Command Line Interface (CLI)
+
 The main functionality of MaRaCluster is provided by the `maracluster` command. This command has several sub-commands to execute different parts of the clustering and merging. The most important ones are `maracluster batch` and `maracluster consensus`. The first takes a list of ms2 spectra as input and outputs a list of clusters, the second takes one of these outputs and creates consensus spectra for each cluster.
 
 To run `maracluster batch`, a flat text file with the absolute/relative path to each of the ms2 spectrum files (one per line) is needed. Such a file can easily be generated using a `ls -1` command, *e.g.* `ls -1 ms2/* > files.txt`. Any ms2 spectrum format readable by ProteoWizard can be used as input. Use the following command to start clustering:

admin/builders/centos64_build.sh

@@ -28,7 +28,7 @@ fi
 
 rm -f $build_dir/{maracluster,maracluster-gui}/mar*.rpm
 
-sudo yum install -y gcc gcc-c++ rpm-build cmake
+sudo yum install -y gcc gcc-c++ rpm-build cmake rsync
 CMAKE_BINARY=cmake # this can be overridden if a newer version of cmake is needed
 
 mkdir -p ${build_dir}/tools

admin/builders/install_proteowizard.sh

@@ -44,11 +44,9 @@ echo "Building ProteoWizard and Boost, this may take some time.."
 find build-*-x86_64/ -type f | grep -i libboost_regex-.*\.a$ | xargs -I{} cp {} ../lib
 find build-*-x86_64/ -type f | grep -i libboost_program_options-.*\.a$ | xargs -I{} cp {} ../lib
 
-cd libraries/zlib-1.2.3
-find ./ -type f | grep -i '.h$\|.hpp$' | xargs -I{} cp --parents {} ../../../include/
-cd ../../
-rsync -ap libraries/boost_aux/boost/ ../include/boost
-rsync -ap --include '*.ipp' --exclude '*' libraries/boost_1_67_0/boost/ ../include/boost
+rsync -ap --include "*/" --include "*.h" --include "*.hpp" --exclude "*"  libraries/zlib-1.2.3/ ../include/zlib
+rsync -ap --include "*/" --include "*.h" --include "*.hpp" --exclude "*" libraries/boost_aux/boost/ ../include/boost
+rsync -ap --include "*/" --include '*.ipp' --exclude '*' libraries/boost_1_67_0/boost/ ../include/boost
 
 # the boost libraries' naming convention does not always work well with cmake, so we force a more simple naming convention
 ln -s -f ../lib/libboost_system-*.a ../lib/libboost_system.a

admin/builders/install_qt.sh

@@ -13,18 +13,18 @@ if [ ! -d Qt-dynamic ]; then
   tar xf ${linux_qt}.tar.xz
   cd ${linux_qt}
 
-  ./configure -prefix ${tools_dir}/Qt-dynamic -opensource -confirm-license -nomake tools -nomake examples -nomake tests
+  ./configure -prefix ${tools_dir}/Qt-dynamic -opensource -confirm-license -nomake tools -nomake examples -nomake tests -release > ../qt_config.log 2>&1
 
   echo "Building Qt base, this may take some time.."
 
-  make -j4 > ../qt_installation.log 2>&1
-  make install -j4
+  make -j4 > ../qt_build.log 2>&1
+  make install -j4 > ../qt_install.log 2>&1
 fi
 
 cd ${tools_dir}
 
 # Qt5 requires CMake >= 3.5
-function version_lt() { test "$(echo "$@" | tr " " "\n" | (sort -rV || gsort -rV | head -n 1)" != "$1"; }
+function version_lt() { test "$(echo "$@" | tr " " "\n" | (sort -rV || gsort -rV) | head -n 1)" != "$1"; }
 
 if version_lt $(cmake --version | head -n1 | cut -f3 -d ' ') "3.5"; then
   wget https://github.com/Kitware/CMake/releases/download/v3.13.3/cmake-3.13.3-Linux-x86_64.sh

admin/vagrant/batch.sh

@@ -1,34 +1,34 @@
 #!/bin/bash
 export LANG=en_US.UTF-8
 export LC_ALL="en_US.UTF-8"
-release_dir=${HOME}/release
-
-echo "Building Ubuntu binaries"
-./manager.sh -p ubuntu -r ${release_dir}/ubuntu64 > ubuntu_output.txt 2>&1
-if [[ $? -eq 0 ]]; then
-  echo "Building of Ubuntu binaries succeeded"
-fi
+trap 'echo "Batch script killed"; exit 1' INT TERM
 
-echo "Building Fedora binaries"
-./manager.sh -p fedora -r ${release_dir}/fedora64  > fedora_output.txt 2>&1
-if [[ $? -eq 0 ]]; then
-  echo "Building of Fedora binaries succeeded"
-fi
+release_dir=${HOME}/release
 
-echo "Building CentOS binaries"
-./manager.sh -p centos -r ${release_dir}/centos64  > centos_output.txt 2>&1
-if [[ $? -eq 0 ]]; then
-  echo "Building of CentOS binaries succeeded"
-fi
+platforms=()
+platforms+=(osx)
+#platforms+=(win64)
+#platforms+=(win32)
+#platforms+=(centos)
+#platforms+=(fedora)
+#platforms+=(ubuntu)
 
-echo "Building native 64-bit Windows binaries"
-./manager.sh -p nw64 -r ${release_dir}/win64  > nw64_output.txt 2>&1
-if [[ $? -eq 0 ]]; then
-  echo "Building of native 64-bit Windows binaries succeeded"
-fi
+for platform in ${platforms[@]}; do
+  echo "Building $platform binaries"
+  ./manager.sh -p $platform -r ${release_dir}/$platform > ${platform}_output.txt 2>&1
+  if [[ $? -eq 0 ]]; then
+    echo "Building of ${platform} binaries succeeded"
+  else
+    echo "Building of ${platform} binaries failed"
+  fi
+done
 
-echo "Building native 32-bit Windows binaries"
-./manager.sh -p nw32 -r ${release_dir}/win32  > nw32_output.txt 2>&1
-if [[ $? -eq 0 ]]; then
-  echo "Building of native 32-bit Windows binaries succeeded"
-fi
+# for the osx build, root priviliges are necessary but we can skip the password prompt:
+# Vagrant NFS access https://www.vagrantup.com/docs/synced-folders/nfs.html#root-privilege-requirement
+# add the following lines with $sudo visudo
+#Cmnd_Alias VAGRANT_EXPORTS_CHOWN = /bin/chown 0\:0 /tmp/*
+#Cmnd_Alias VAGRANT_EXPORTS_MV = /bin/mv -f /tmp/* /etc/exports
+#Cmnd_Alias VAGRANT_NFSD_CHECK = /etc/init.d/nfs-kernel-server status
+#Cmnd_Alias VAGRANT_NFSD_START = /bin/systemctl start nfs-server.service
+#Cmnd_Alias VAGRANT_NFSD_APPLY = /usr/sbin/exportfs -ar
+#%sudo ALL=(root) NOPASSWD: VAGRANT_EXPORTS_CHOWN, VAGRANT_EXPORTS_MV, VAGRANT_NFSD_CHECK, VAGRANT_NFSD_START, VAGRANT_NFSD_APPLY

admin/vagrant/manager.sh

@@ -13,7 +13,7 @@ usage: $0
                   [[-h]] [[-a]]
                   [[-b branch]]|[[-s source_directory]]
                   [[-r release_directory]]
-                  -p ubuntu|centos|fedora|nw32|nw64
+                  -p ubuntu|centos|fedora|win32|win64|osx
 
 If no branch and source_directory is provided, the source
 code from which the sourcecode is checked out from will be used.
@@ -61,14 +61,14 @@ while getopts “hab:s:r:p:” OPTION; do
                     vagbox_url=""
                     package_ext="rpm"
                     ;;
-                nw32) 
+                win32) 
                     post="nativew32"
                     batfile=true
                     vagbox_name="win10vs15"
                     vagbox_url="~/VagrantWin7/win10vs15.box"
                     package_ext="exe"
                     ;;
-                nw64) 
+                win64) 
                     post="nativew64"
                     batfile=true
                     vagbox_name="win10vs15"
@@ -181,7 +181,7 @@ Vagrant.configure("2") do |config|
   config.vm.box = "${vagbox_name}"
   config.vm.box_url = "${vagbox_url}"
   config.ssh.insert_key = false
-  config.ssh.password = "vagrant" # private key authentication does not work on this box
+  #config.ssh.password = "vagrant" # private key authentication does not work on this box
   config.vm.boot_timeout = 600
   config.vm.network "private_network", ip: "192.168.56.10"
   
@@ -239,7 +239,7 @@ Vagrant.configure("2") do |config|
   end
   config.vm.provision :shell do |shell|
     shell.path = "${tmp_dir}/${builder}"
-    shell.args = "-s /vagrant/src -r /vagrant/"
+    shell.args = "-s /vagrant/src -b /vagrant/build -r /vagrant/"
   end
 end
 EOF
@@ -295,6 +295,7 @@ if [[ $? -eq 0 ]] && [[ -z ${alive} ]]; then
   vagrant destroy -f
 else
   echo "-a option set or encountered error: keeping the VM alive, remember to close and delete the VM manually."
+  exit 1
 fi
 
 #---------------------------------------------------------------------------------------

src/qt-gui/CMakeLists.txt

@@ -2,14 +2,14 @@ cmake_minimum_required(VERSION 3.5)
 project(MARACLUSTER_GUI)
 set(MARACLUSTER_GUI_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 
-if (UNIX)
+if (APPLE)
+  set(MARACLUSTER_BIN_DESTINATION maracluster-gui.app/Contents/MacOS)
+elseif (UNIX)
   set(CMAKE_INSTALL_RPATH "$ORIGIN")
   set(MARACLUSTER_BIN_DESTINATION lib/maracluster)
-elseif (APPLE)
-  set(MARACLUSTER_BIN_DESTINATION maracluster-gui.app/Contents/MacOS)
 elseif (MSVC)
   set(MARACLUSTER_BIN_DESTINATION bin)
-endif (UNIX)
+endif (APPLE)
 
 # get the maracluster executable
 set(SKIP_MAIN_CPACK ON)