Merge pull request #21505 from boegel/20240930191938_new_pr_GATK4600

{bio}[GCCcore/13.2.0] GATK v4.6.0.0 w/ Java 17

easybuild/easyconfigs/g/GATK/GATK-4.6.0.0-GCCcore-13.2.0-Java-17.eb

@@ -0,0 +1,55 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB
+# Authors::   George Tsouloupas <[email protected]>, Fotis Georgatos <[email protected]>,
+#             Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+# Modified by: Adam Huffman, Jonas Demeulemeester
+# The Francis Crick Institute
+# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen
+# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT
+# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV
+##
+
+easyblock = 'Tarball'
+
+name = 'GATK'
+version = '4.6.0.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.broadinstitute.org/gatk/'
+description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
+ to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
+ with a primary focus on variant discovery and genotyping as well as strong emphasis on
+ data quality assurance. Its robust architecture, powerful processing engine and
+ high-performance computing features make it capable of taking on projects of any size."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
+sources = ['gatk-%(version)s.zip']
+checksums = ['a5d31e34630f355e5a119894f2587fec47049fedff04300f6633c31ef14c3a66']
+
+dependencies = [
+    ('Java', '17', '', SYSTEM),
+    ('Python', '3.11.5'),
+]
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ['gatk'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "gatk --help",
+    "gatk --list",
+]
+
+moduleclass = 'bio'