add file check to templates; add dark theme

mjoppich · May 6, 2019 · 4117c43 · 4117c43
1 parent ccf37da
commit 4117c43
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Showing 23 changed files with 593 additions and 10 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -228,6 +228,12 @@ file(GLOB DUKTAPE
         "src/duktape/*"
         )
 
+file(GLOB DSTYLE
+    "dstyle/*"
+    "dstyle/framelesswindow/*"
+    )
+
+
 add_project_meta(META_FILES_TO_INCLUDE)
 
 set(RESOURCE_FILES "${PROJECT_NAME}.qrc")
@@ -258,8 +264,8 @@ endif()
 
 
 add_executable(${PROJECT_NAME} ${OS_BUNDLE} # Expands to WIN32 or MACOS_BUNDLE depending on OS
-    ${bioGUI_H} ${bioGUIapp_H} ${bioGUI_SRC} ${parsinglib_SRC} ${parsinglib_H} ${parsinglib_nodes_H} ${META_FILES_TO_INCLUDE} ${RESOURCE_FILES}
-    ${DUKTAPE}                           
+    ${DSTYLE} ${bioGUI_H} ${bioGUIapp_H} ${bioGUI_SRC} ${parsinglib_SRC} ${parsinglib_H} ${parsinglib_nodes_H} ${META_FILES_TO_INCLUDE} ${RESOURCE_FILES}
+    ${DUKTAPE} "./dstyle/darkstyle.qrc" "./dstyle/framelesswindow.qrc"
 )
 
 
@@ -275,6 +281,9 @@ ADD_LIBRARY(lualib STATIC IMPORTED)
 SET_TARGET_PROPERTIES(lualib PROPERTIES IMPORTED_LOCATION "${LUA_LIBRARY}")
 
 target_include_directories(${PROJECT_NAME} PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/dstyle")
+target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/dstyle/framelesswindow")
+
 TARGET_LINK_LIBRARIES(${PROJECT_NAME} openssl_crypto openssl_ssl lualib ${CMAKE_DL_LIBS} )
 
 qt5_use_modules(${PROJECT_NAME} Core Gui Widgets Network Xml XmlPatterns)

diff --git a/install_templates/install_albacore.igui b/install_templates/install_albacore.igui
@@ -38,6 +38,37 @@ if [ "$3" = "1" ]; then
     fi
 fi
 
+APPBINARYESC="$PYTHON_BIN_DIR}/"
+APPBINARY="${PYTHON_BIN_DIR}/read_fast5_basecaller.py"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
 if [ "$4" != "0" ]; then
 
 IP=$4

diff --git a/install_templates/install_ballgown.igui b/install_templates/install_ballgown.igui
@@ -125,6 +125,36 @@ print("Finished")
 
 BALLGOWNSTATTEST
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/statTest.R"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
 
 if [ $# -eq 5 ]; then
 

diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -63,6 +63,37 @@ if [ $# -gt 2 ]; then
 
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/bowtie"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
 if [ $# -eq 5 ]; then
 
 IP=$4

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -60,6 +60,38 @@ if [ $# -gt 2 ]; then
 
 fi
 
+
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/bowtie2"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
 if [ $# -eq 5 ]; then
 
 IP=$4

diff --git a/install_templates/install_bwa.igui b/install_templates/install_bwa.igui
@@ -67,6 +67,37 @@ if [ $# -gt 2 ]; then
 
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/bwa"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
 if [ $# -eq 5 ]; then
 
 IP=$4

diff --git a/install_templates/install_canu.igui b/install_templates/install_canu.igui
@@ -70,7 +70,36 @@ if [ $# -gt 2 ]; then
 	fi
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/canu"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
 
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
 
 if [ $# -eq 5 ]; then
 

diff --git a/install_templates/install_featurecounts.igui b/install_templates/install_featurecounts.igui
@@ -72,7 +72,36 @@ if [ $# -gt 2 ]; then
    fi
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/featureCounts"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
 
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
 
 if [ $# -eq 5 ]; then
 

diff --git a/install_templates/install_glimmer.igui b/install_templates/install_glimmer.igui
@@ -72,6 +72,37 @@ if [ $# -gt 2 ]; then
 
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/scripts/g3-from-training.csh"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
 if [ $# -eq 5 ]; then
 
 # fix scripts

diff --git a/install_templates/install_graphmap.igui b/install_templates/install_graphmap.igui
@@ -68,7 +68,36 @@ if [ $# -gt 2 ]; then
    fi
 fi
 
+APPBINARYESC="${PROGDIRESC}/${PROG}/bin/Linux-x64/"
+APPBINARY="${PROGDIRESC}/${PROG}/bin/Linux-x64/graphmap"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
 
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
 
 if [ $# -eq 5 ]; then
 
@@ -137,7 +166,7 @@ $NCCMD <<EOF
        <label>Threads</label><input id="graphmap_threads" type="int">4</input>
     </group>
 
-    <streambox id="output1">
+    <streambox linebreaks="TRUE" id="output1">
       <stream id="outputstream1">OS1</stream>
       <stream id="outputstream2">OS2</stream>
     </streambox>