Merge branch 'master' of http://github.com/mjoppich/biogui

CMakeLists.txt

@@ -500,17 +500,24 @@ endif()
         endif()
 
 
-        if (UNIX AND NOT APPLE AND FALSE)
+        if (UNIX AND NOT APPLE)
             get_filename_component(QT5GUI_DIR ${Qt5_GuiLocation} DIRECTORY)
 
             add_custom_command( TARGET ${PROJECT_NAME} POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${QT5GUI_DIR}/libicudata.so.56 ${PROJECT_BINARY_DIR})
             add_custom_command( TARGET ${PROJECT_NAME} POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${QT5GUI_DIR}/libicui18n.so.56 ${PROJECT_BINARY_DIR})
             add_custom_command( TARGET ${PROJECT_NAME} POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${QT5GUI_DIR}/libicuuc.so.56 ${PROJECT_BINARY_DIR})
+
+            add_custom_command( TARGET ${PROJECT_NAME} POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${QT5GUI_DIR}/libQt5DBus.so.5 ${PROJECT_BINARY_DIR})
+            add_custom_command( TARGET ${PROJECT_NAME} POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${QT5GUI_DIR}/libQt5XcbQpa.so.5 ${PROJECT_BINARY_DIR})
 
+
+
 			file(GLOB biogui_linux_libs
 					${QT5GUI_DIR}/libicudata.so.56
 					${QT5GUI_DIR}/libicui18n.so.56
 					${QT5GUI_DIR}/libicuuc.so.56
+                                        ${QT5GUI_DIR}/libQt5DBus.so.5
+                                        ${QT5GUI_DIR}/libQt5XcbQpa.so.5
 					)
 
 

install_templates/install_albacore.igui

@@ -45,7 +45,16 @@ PORT=$5
 
 echo "Sending Template to $IP at $PORT"
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
 
 <template description="albacore basecaller aligner" title="albacore (python)">
 <window title="albacore basecaller">

install_templates/install_apple_first.igui

@@ -11,7 +11,10 @@ if [ "$(uname)" == "Darwin" ]; then
 
 		echo "Installing brew"
 		yes "$2" | /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
-
+
+        echo "Installing wget and netcat"
+		brew install wget netcat
+
 		echo "Enjoy bioGUI!"
 	else
 		echo "No sudo password, not installing dependencies"

install_templates/install_ballgown.igui

@@ -1,24 +1,33 @@
 #! Install Ballgown 1.0.1
 
-DEP_PACKAGES="R zlibc zlib1g zlib1g-dev libxml2-dev libcurl4-openssl-dev"
-
-echo "Dependencies: $DEP_PACKAGES R: devtools, RSkittleBrewer, ballgown"
 if [ ! "$2" = "" ]; then
 
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get install $DEP_PACKAGES
-
-	RLIBSUSER=`Rscript -e "cat(Sys.getenv('R_LIBS_USER'))"`
-	mkdir -p $RLIBUSER
-
-	Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); install.packages(\"devtools\"); devtools::install_github('alyssafrazee/RSkittleBrewer'); biocLite(\"ballgown\", lib.loc=Sys.getenv('R_LIBS_USER'), lib=Sys.getenv('R_LIBS_USER'));"
+    if [ "$(uname)" == "Darwin" ]; then
 
-else
-	echo "No sudo password, not installing dependencies"
-	echo "Did not install ballgown. Hoping for the best!"
+        echo "Installing brew gnuplot"
+        brew install r libxml2 libxml2 zlib
+
+    else
 
+        DEP_PACKAGES="R zlibc zlib1g zlib1g-dev libxml2-dev libcurl4-openssl-dev"
+
+        echo "Dependencies: $DEP_PACKAGES R: devtools, RSkittleBrewer, ballgown"
+        echo $2 | sudo -S apt-get update
+        echo $2 | sudo -S apt-get install $DEP_PACKAGES
+
+    fi
+
+else
+   echo "No sudo password, not installing dependencies"
 fi
 
+echo "options(repos = c(CRAN = "https://cran.rstudio.com"))" > ~/.Rprofile
+
+RLIBSUSER=`Rscript -e "cat(Sys.getenv('R_LIBS_USER'))"`
+mkdir -p $RLIBUSER
+
+Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); install.packages(\"devtools\"); devtools::install_github('alyssafrazee/RSkittleBrewer'); biocLite(\"ballgown\", lib.loc=Sys.getenv('R_LIBS_USER'), lib=Sys.getenv('R_LIBS_USER'));"
+
 RSCRIPT=`which Rscript`
 
 ## set all variables
@@ -30,8 +39,8 @@ if [ -z "${PROGDIR}" ]; then
 	PROGDIR=~/bioGUI/progs/
 fi
 
-PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/
+PROGDIRESC=$(echo "$PROGDIR" | sed 's/ /\\ /g')
+APPBINARYDIR="${PROGDIR}/${PROG}/"
 
 ## create progdir
 mkdir -p "$PROGDIR/$PROG"
@@ -122,7 +131,16 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
 
 <template description="Ballgown: Isoform-level differential expression analysis in R." title="${PROGNICE}">
 <window title="${PROGNICE}">

install_templates/install_bowtie1.igui

@@ -57,7 +57,16 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
 
 <template description="bowtie 1.1.2 aligner" title="bowtie 1.1.2">
 <window title="bowtie 1.1.2 aligner">

install_templates/install_bowtie2.igui

@@ -57,7 +57,16 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
 
 <template description="bowtie2 2.0.4 aligner" title="bowtie2 2.0.4">
 <window title="bowtie2 2.0.4 aligner">

install_templates/install_canu.igui

@@ -1,19 +1,25 @@
 #! Install canu (github)
 
-echo "This tool will not compile in folders where the absolute path contains spaces!"
-echo "Dependencies: None"
-
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-  echo $2 | sudo -S apt-get update
-  echo $2 | sudo -S apt-get -y install gnuplot
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gnuplot"
+        brew install gnuplot --with-cairo
+
+    else
+
+        echo "Installing dependencies"
+        echo $2 | sudo -S apt-get update
+        echo $2 | sudo -S apt-get -y install gnuplot
+
+    fi
 
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 
-
 ## set all variables
 PROG=canu
 PROGDIR=$1
@@ -26,7 +32,16 @@ fi
 
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/Linux-amd64/bin/
+APPBINARYDIR=${PROGDIR}/${PROG}/Linux-amd64/bin/
+
+
+if [ "$(uname)" == "Darwin" ]; then
+    APPBINARYDIR=${PROGDIR}/${PROG}/Darwin-amd64/bin/
+else
+    APPBINARYDIR=${PROGDIR}/${PROG}/Linux-amd64/bin/
+fi
+
+
 
 if [ -d "$PROGDIR/$PROG" ]; then
     echo "Removing Folder $PROGDIR/$PROG"
@@ -64,7 +79,16 @@ PORT=$5
 
 echo "Sending Template to $IP at $PORT"
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
 
 <!--<?xml version="1.0" encoding="UTF-8")>-->
 

install_templates/install_glimmer.igui

@@ -1,27 +1,40 @@
 #! Install glimmer302b
 
-echo "This tool will not compile in folders where the absolute path contains spaces!"
 
 echo "Dependencies: csh"
 if [ ! "$2" = "" ]; then
-	echo "Installing dependencies"
-	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install csh
-
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "This tool will not compile if install directory path contains spaces!"
+
+    else
+
+        echo "Installing Dependencies (aptitude/Ubuntu)"
+
+        echo "Installing dependencies"
+        echo $2 | sudo -S apt-get update
+        echo $2 | sudo -S apt-get -y install csh
+
+    fi
+
 else
-	echo "No sudo password, not installing dependencies"
+   echo "No sudo password, not installing dependencies"
 fi
 
 ## set all variables
 PROG=glimmer302b
 PROGDIR=$1
 
 if [ -z "${PROGDIR}" ]; then
-	PROGDIR=~/bioGUI/progs/
+   PROGDIR=~/bioGUI/progs/
 fi
 
-PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/
+PROGDIRESC=$(echo "$PROGDIR" | sed 's/ /\\ /g')
+
+echo "PROGDIRESC $PROGDIRESC"
+
+APPBINARYDIR="${PROGDIRESC}/${PROG}/"
 
 ## create progdir
 mkdir -p "$PROGDIR/$PROG"
@@ -35,24 +48,35 @@ tar -xzf "$PROG.tar.gz" --strip 1 -C "$PROGDIR/$PROG"
 #install prog
 cd "$PROGDIR/$PROG/src"
 
+
+# this fixes some issues on mac, not all
+for script in **/Makefile; do
+
+echo "Escaping $script"
+sed -i.bak "s/cd \.\.\/\.\.\; pwd/cd \.\.\/\.\.\; pwd \| sed \'s\/ \/\\\\\\\\ \/g\'/g" $script
+
+done
+
+sed -i.bak "s/cd \.\.\; pwd/cd \.\.; pwd \| sed \'s\/ \/\\\\\\\\ \/g\'/g" Makefile
+
 make
 
 if [ $# -gt 2 ]; then
 
-	if [ "$3" = "1" ]; then
+   if [ "$3" = "1" ]; then
 
-		if ! grep -q "$PROGDIRESC/$PROG" ~/.bashrc; then
-			echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
-		fi
-	fi
+      if ! grep -q "$PROGDIRESC/$PROG" ~/.bashrc; then
+         echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
+      fi
+   fi
 
 fi
 
 if [ $# -eq 5 ]; then
 
 # fix scripts
 
-for script in $PROGDIR/$PROG/scripts/*.csh; do
+for script in $PROGDIRESC/$PROG/scripts/*.csh; do
 
 sed -i "/set awkpath = /c\set awkpath = $PROGDIRESC/$PROG/scripts/" $script
 sed -i "/set glimmerpath = /c\set glimmerpath = $PROGDIRESC/$PROG/bin/" $script
@@ -65,7 +89,17 @@ echo "sending template"
 IP=$4
 PORT=$5
 
-nc -q 0 $IP $PORT <<EOF
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
+
 <!--<?xml version="1.0" encoding="UTF-8")>-->
 <template description="Glimmer3 scripts ($PROG)" title="Glimmer3">
 
@@ -74,7 +108,7 @@ nc -q 0 $IP $PORT <<EOF
 
    <label>Run Program in WSL?</label>
    <checkbox id="WSLsel" value="true" selectonwindows="true">WSL</checkbox>
-      
+
     <group title="Operation" exclusive="true">
 
 <group id="fromscratch" title="From Scratch" checkable="true">
@@ -97,14 +131,14 @@ nc -q 0 $IP $PORT <<EOF
 
 
 
-    <action id="runprog" hint="click here to run program">run program</action>  
-  
+    <action id="runprog" hint="click here to run program">run program</action>
+
     <streambox id="output1">
       <stream id="outputstream1">OS1</stream>
       <stream id="outputstream2">OS2</stream>
     </streambox>
 
-  
+
   </vgroup>
 </window>
 
@@ -132,11 +166,11 @@ nc -q 0 $IP $PORT <<EOF
     <output type="STD" color="green" to="outputstream1" />
 </execute>
 </if>
-  
+
 </execution>
 </template>
 
 EOF
 
 
-fi
+fi