biology/gatk: Update 4.1.3.0 -> 4.1.4.1

svn path=/head/; revision=523602

biology/gatk/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	gatk
-DISTVERSION=	4.1.3.0
+DISTVERSION=	4.1.4.1
 CATEGORIES=	biology java
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 

biology/gatk/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1578219311
-SHA256 (gatk-4.1.3.0-deps.tar.gz) = 5258f2ed0faebb16fed888cb5ae688f833b7ff9e293f89e0c0cee33670ac7fbe
-SIZE (gatk-4.1.3.0-deps.tar.gz) = 250818646
-SHA256 (broadinstitute-gatk-4.1.3.0_GH0.tar.gz) = f24e7dcb56e16a8aa81e12bdd87916de985c2a1089d6fc4b1a5cdb517e4e9f9c
-SIZE (broadinstitute-gatk-4.1.3.0_GH0.tar.gz) = 64567278
+TIMESTAMP = 1579483921
+SHA256 (gatk-4.1.4.1-deps.tar.gz) = b634903f674aa1550039c4434e0ef0efab75d509e80d5073a2b5f3a0120fd68e
+SIZE (gatk-4.1.4.1-deps.tar.gz) = 253677476
+SHA256 (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 54129c3973ad7f1c501ecd7c841d15cd09fdd0d5ca3057810c17d7b7b9d88eb7
+SIZE (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 64600068

biology/gatk/files/patch-build.gradle

@@ -1,6 +1,6 @@
---- build.gradle.orig	2018-10-23 15:15:16 UTC
+--- build.gradle.orig	2019-11-26 15:07:28 UTC
 +++ build.gradle
-@@ -115,7 +115,7 @@ def resolveLargeResourceStubFiles(largeR
+@@ -114,7 +114,7 @@ def resolveLargeResourceStubFiles(largeResourcesFolder
      }
  
      // check for stub files, try to pull once if there are any, then check again
@@ -9,16 +9,16 @@
          final gitLFSPullLargeResources = "git lfs pull --include $largeResourcesFolder"
          execGitLFSCommand(gitLFSPullLargeResources)
          if (checkForLFSStubFiles(largeResourcesFolder)) {
-@@ -135,7 +135,7 @@ def ensureBuildPrerequisites(requiredJav
-                 "The ClassLoader obtained from the Java ToolProvider is null. "
-                 + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage")
+@@ -148,7 +148,7 @@ def ensureBuildPrerequisites(largeResourcesFolder, bui
+     if (!JavaVersion.current().isJava8() && !JavaVersion.current().isJava11()) {
+         println("Warning: using Java ${JavaVersion.current()} but only Java 8 and Java 11 have been tested.")
      }
--    if (!file(".git").isDirectory()) {
-+    if (false && !file(".git").isDirectory()) {
-         throw new GradleException("The GATK Github repository must be cloned using \"git clone\" to run the build. "
-                 + "$buildPrerequisitesMessage")
-     }
-@@ -366,7 +366,7 @@ def createGatkSymlinks(destinationDir, a
+-    if (!looksLikeWereInAGitRepository()) {
++    if (false && !looksLikeWereInAGitRepository()) {
+         throw new GradleException("This doesn't appear to be a git folder. " +
+                 "The GATK Github repository must be cloned using \"git clone\" to run the build. " +
+                 "\n$buildPrerequisitesMessage")
+@@ -396,7 +396,7 @@ def createGatkSymlinks(destinationDir, archivePath, su
  }
  
  final isRelease = Boolean.getBoolean("release")

biology/gatk/pkg-descr

@@ -10,4 +10,4 @@ offers a wide variety of tools with a primary focus on variant discovery and
 genotyping. Its powerful processing engine and high-performance computing
 features make it capable of taking on projects of any size.
 
-WWW: https://software.broadinstitute.org/gatk/
+WWW: https://gatk.broadinstitute.org/hc/en-us