JAL-2629 can now choose number of jackhmmer iterations

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index 07a4095..a7c7f18 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -49,7 +49,7 @@ def compile_target_compatibility
 ext {
   // where the getdown channel will be built.
   // TODO: consider allowing this expression to  be overrriden by -P arg
-  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
+  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
   getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
   getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
   getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
@@ -538,6 +538,8 @@ task compileLinkCheck(type: JavaCompile) {
   destinationDir = file("$jalviewDir/$utilsDir")
   source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
+  inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java")
   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 }
@@ -550,7 +552,6 @@ task linkCheck(type: JavaExec) {
   workingDir = jalviewDir
   def help = "$classes/$helpDir"
   args = [ "$classes/$helpDir", "-nointernet" ]
-  //args = [ "$classesDir/$helpDir", "-nointernet" ]
 
   doFirst {
     helplinkscheckeroutputfile.createNewFile()
@@ -648,7 +649,7 @@ task getdownWebsite() {
     props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
 
     if (getdown_local == "true") {
-      getdown_app_base = "file://"+file(getdownWebsiteDir).getAbsolutePath()
+      getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     }
     props.put("getdown_txt_appbase", getdown_app_base)
     props.each{ prop, val ->
@@ -846,15 +847,26 @@ task copyInstall4jTemplate(type: Copy) {
   outputs.files(install4jConf)
 
   doLast {
+    // include file associations in installer
     def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
     ant.replaceregexp(
       byline: false,
       flags: "s",
       match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
-      //match: '<action.*?EXTENSIONS_REPLACED_BY_GRADLE.*?</action>',
       replace: installerFileAssociationsXml,
       file: install4jConf
     )
+    /*
+    // include uninstaller applescript app files in dmg
+    def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+      replace: installerDMGUninstallerXml,
+      file: install4jConf
+    )
+    */
   }
 }