gatk package: new versions, updated helper script (#10459)

Closes #10168

* Add versions 4.1.0.0 and 4.0.12.0
* Replace md5 checksums with sha256
* Logic to generate a helper script for versions earlier than 4 was
  not running. This corrects the branch which controls whether this
  script is generated.
* Constrain Java dependency to version 8 (GATK does not work with
  Java 11)
* Avoid adding scripts that have dependencies not handled by Spack
  such as gcloud and google-chrome. These scripts are good candidates
  for later extensions.

1 files changed, 76 insertions, 44 deletions

diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
index 5b1d862812..f9d6ff0414 100644
--- a/var/spack/repos/builtin/packages/gatk/package.py
+++ b/var/spack/repos/builtin/packages/gatk/package.py
@@ -3,59 +3,91 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack import *
 import os.path
+import glob
+from spack import *
 
 
 class Gatk(Package):
-    """Genome Analysis Toolkit
-       Variant Discovery in High-Throughput Sequencing Data
     """
+    Genome Analysis Toolkit
+    Variant Discovery in High-Throughput Sequencing Data
+    """
+
     homepage = "https://software.broadinstitute.org/gatk/"
-    url      = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
-
-    version('4.0.11.0', sha256='5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536')
-    version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
-            url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
-    version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
-            url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
-    version('3.8-1', 'a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c', extension='tar.bz2',
-            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef")
-    version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
-            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
-
-    depends_on('java@8:', type='run')
-    depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
-    depends_on('r@3.2:', type='run', when='@4.0:')
+    url = "https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip"
+    list_url = "https://github.com/broadinstitute/gatk/releases"
+
+    version(
+        "4.1.0.0",
+        sha256="148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d",
+    )
+    version(
+        "4.0.12.0",
+        sha256="733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f",
+    )
+    version(
+        "4.0.11.0",
+        sha256="5ee23159be7c65051335ac155444c6a49c4d8e3515d4227646c0686819934536",
+    )
+    version(
+        "4.0.8.1",
+        sha256="e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9",
+    )
+    version(
+        "4.0.4.0",
+        sha256="801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4",
+    )
+    version(
+        "3.8-1",
+        "a0829534d2d0ca3ebfbd3b524a9b50427ff238e0db400d6e9e479242d98cbe5c",
+        extension="tar.bz2",
+        url="https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef",
+    )
+    version(
+        "3.8-0",
+        "0581308d2a25f10d11d3dfd0d6e4d28e",
+        extension="tar.gz",
+        url="https://software.broadinstitute.org/gatk/download/auth?package=GATK",
+    )
+
+    depends_on("java@8", type="run")
+    depends_on("python@2.6:2.8,3.6:", type="run", when="@4.0:")
+    depends_on("r@3.2:", type="run", when="@4.0:")
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
 
-        # Install all executable non-script files to prefix bin
-        jar_file = 'GenomeAnalysisTK.jar'
-        install(jar_file, prefix.bin)
-
-        # Skip helper script settings
-        if spec.satisfies('@:4.0'):
-            return
-
-        # Set up a helper script to call java on the jar file,
-        # explicitly codes the path for java and the jar file.
-        script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
-        script = join_path(prefix.bin, "gatk")
-        install(script_sh, script)
-        set_executable(script)
-
-        # Munge the helper script to explicitly point to java and the
-        # jar file.
-        java = join_path(self.spec['java'].prefix, 'bin', 'java')
-        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
-        filter_file('^java', java, script, **kwargs)
-        filter_file('GenomeAnalysisTK.jar', join_path(prefix.bin,
-                    'GenomeAnalysisTK.jar'),
-                    script, **kwargs)
+        # For ver 3.x will install "GenomeAnalysisTK.jar"
+        # For ver 4.x will install both "gatk-package-<ver>-local.jar"
+        # and "gatk-package-<ver>-spark.jar"
+        for file in glob.glob("*.jar"):
+            install(file, prefix.bin)
+
+        # Skip helper script for versions >4.0
+        if spec.satisfies("@4.0:"):
+            install("gatk", prefix.bin)
+        else:
+            # Set up a helper script to call java on the jar file,
+            # explicitly codes the path for java and the jar file.
+            script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
+            script = join_path(prefix.bin, "gatk")
+            install(script_sh, script)
+            set_executable(script)
+
+            # Munge the helper script to explicitly point to java and the
+            # jar file.
+            java = join_path(self.spec["java"].prefix, "bin", "java")
+            kwargs = {"ignore_absent": False, "backup": False, "string": False}
+            filter_file("^java", java, script, **kwargs)
+            filter_file(
+                "GenomeAnalysisTK.jar",
+                join_path(prefix.bin, "GenomeAnalysisTK.jar"),
+                script,
+                **kwargs
+            )
 
     def setup_environment(self, spack_env, run_env):
-        run_env.prepend_path('GATK',
-                             join_path(self.prefix, 'bin',
-                                                    'GenomeAnalysisTK.jar'))
+        run_env.prepend_path(
+            "GATK", join_path(self.prefix, "bin", "GenomeAnalysisTK.jar")
+        )